diff --git a/summaries/2026_june_08/README.md b/summaries/2026_june_08/README.md new file mode 100644 index 0000000..92852f4 --- /dev/null +++ b/summaries/2026_june_08/README.md @@ -0,0 +1,79 @@ +# Summary 2026 June 08 +- Number of Datasets: 61 +- Number of Ligands: 961 +- Number of Edges: 1624 +- Total Wallclock Time: 207.50 Hours +- Average Time Per Edge: 0.13 Hours +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) + + +## Description +Evalutes changing the REST region to only include rings that are connected to dummy atoms (https://github.com/tmd-industries/tmd/pull/133) + + +![Retrospective dG performance](dg_plot.png) + +## Dataset Metrics +| set | dataset | N | Kendall 𝜏 | MUE | RMSE | R² | Spearman ρ | +| :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | +| jacs_set | Thrombin | 11 | 0.60 | 0.62 | 0.72 | 0.85 | 0.78 | +| jacs_set | Bace | 36 | 0.31 | 1.21 | 1.51 | 0.20 | 0.44 | +| jacs_set | Mcl1 | 42 | 0.48 | 1.45 | 1.90 | 0.44 | 0.66 | +| jacs_set | Jnk1 | 21 | 0.57 | 1.29 | 1.47 | 0.51 | 0.71 | +| jacs_set | Ptp1B | 23 | 0.53 | 1.29 | 2.14 | 0.32 | 0.65 | +| jacs_set | Tyk2 | 16 | 0.67 | 0.40 | 0.50 | 0.84 | 0.84 | +| jacs_set | Cdk2 | 16 | 0.58 | 0.66 | 0.76 | 0.67 | 0.79 | +| jacs_set | P38 | 34 | 0.48 | 1.05 | 1.36 | 0.49 | 0.65 | +| miscellaneous_set | Hiv1 Protease | 13 | -0.09 | 1.36 | 1.64 | 0.09 | -0.12 | +| miscellaneous_set | Faah | 24 | 0.40 | 1.58 | 1.80 | 0.57 | 0.51 | +| miscellaneous_set | Btk | 6 | 0.60 | 1.80 | 2.19 | 0.71 | 0.71 | +| miscellaneous_set | Cdk8 | 10 | 0.11 | 1.55 | 1.82 | 0.01 | 0.14 | +| miscellaneous_set | Malt1 | 16 | 0.47 | 1.58 | 1.78 | 0.52 | 0.59 | +| miscellaneous_set | Galectin | 26 | 0.50 | 0.90 | 1.24 | 0.60 | 0.70 | +| janssen_bace | Keranen P2 | 12 | 0.08 | 0.61 | 0.71 | 0.08 | 0.11 | +| janssen_bace | Bace Ciordia Prospective | 9 | 0.78 | 1.28 | 1.76 | 0.48 | 0.88 | +| janssen_bace | Bace P3 Arg368 In | 21 | 0.22 | 1.62 | 1.84 | 0.16 | 0.32 | +| janssen_bace | Ciordia Retro | 32 | 0.59 | 1.01 | 1.31 | 0.62 | 0.79 | +| water_set | Chk1 | 13 | -0.43 | 2.29 | 2.97 | 0.03 | -0.45 | +| water_set | Thrombin | 21 | 0.35 | 0.93 | 1.14 | 0.29 | 0.50 | +| water_set | Scyt Dehyd | 7 | 0.52 | 2.10 | 2.63 | 0.64 | 0.71 | +| water_set | Urokinase | 4 | 0.67 | 0.69 | 0.73 | 0.59 | 0.80 | +| water_set | Hsp90 Woodhead | 4 | 0.33 | 1.30 | 1.41 | 0.51 | 0.60 | +| water_set | Hsp90 Kung | 11 | 0.60 | 2.04 | 2.61 | 0.53 | 0.78 | +| water_set | Taf12 | 8 | 0.29 | 0.63 | 0.78 | 0.14 | 0.29 | +| water_set | Brd4 | 8 | 0.14 | 1.35 | 1.69 | 0.02 | -0.02 | +| gpcrs | A2A | 25 | 0.55 | 1.72 | 2.34 | 0.57 | 0.72 | +| gpcrs | P2Y1 Ortho Sub | 12 | 0.75 | 1.19 | 1.46 | 0.92 | 0.88 | +| gpcrs | P2Y1 Meta Sub | 20 | 0.38 | 1.05 | 1.47 | 0.40 | 0.54 | +| merck | Shp2 | 26 | 0.16 | 1.66 | 2.09 | 0.11 | 0.23 | +| merck | Cdk8 | 32 | 0.68 | 1.89 | 2.16 | 0.73 | 0.86 | +| merck | Pfkfb3 | 40 | 0.43 | 0.93 | 1.19 | 0.38 | 0.62 | +| merck | Cmet Charge 1 | 12 | 0.58 | 1.31 | 1.74 | 0.38 | 0.67 | +| merck | Cmet Charge 0 | 12 | 0.66 | 1.15 | 1.46 | 0.82 | 0.78 | +| merck | Hif2A Jmc2023 | 38 | 0.59 | 1.63 | 1.84 | 0.58 | 0.78 | +| merck | Tnks2 Charge 0 | 21 | 0.55 | 0.57 | 0.80 | 0.60 | 0.73 | +| merck | Tnks2 Charge 1 | 6 | 0.47 | 0.60 | 0.68 | 0.45 | 0.66 | +| merck | Syk Charge 0 | 40 | 0.03 | 1.19 | 1.45 | 0.03 | 0.01 | +| merck | Syk Charge -1 | 6 | 0.07 | 0.85 | 1.18 | 0.71 | 0.09 | +| merck | Hif2A | 41 | 0.17 | 1.63 | 1.94 | 0.11 | 0.26 | +| merck | Eg5 Charge 0 | 9 | 0.54 | 0.88 | 1.09 | 0.72 | 0.74 | +| merck | Eg5 Charge 1 | 19 | 0.33 | 0.87 | 1.02 | 0.22 | 0.44 | +| mcs_docking_set | Renin | 29 | 0.38 | 1.41 | 1.86 | 0.26 | 0.51 | +| mcs_docking_set | Hne Charge -1 | 2 | 1.00 | 0.17 | 0.17 | 1.00 | 1.00 | +| mcs_docking_set | Hne Charge 0 | 14 | 0.76 | 0.69 | 0.84 | 0.82 | 0.88 | +| schrodinger_macrocycles | Mht1 | 3 | 1.00 | 1.06 | 1.18 | 0.87 | 1.00 | +| schrodinger_macrocycles | 2Ep9 | 4 | 0.67 | 0.92 | 1.11 | 0.06 | 0.80 | +| schrodinger_macrocycles | 3Rkz | 7 | 0.62 | 1.31 | 1.40 | 0.60 | 0.71 | +| schrodinger_macrocycles | Hsp90 | 10 | 0.56 | 0.83 | 1.01 | 0.70 | 0.73 | +| scaffold_hopping_set | Bace1 | 3 | 1.00 | 1.77 | 1.92 | 0.71 | 1.00 | +| bayer_macrocycles | Ftase | 5 | 0.40 | 0.94 | 0.98 | 0.22 | 0.50 | +| bayer_macrocycles | Brd4 | 3 | 1.00 | 0.55 | 0.66 | 0.89 | 1.00 | +| fragments | Hsp90 Single Ring | 7 | 0.49 | 0.77 | 0.94 | 0.39 | 0.63 | +| fragments | Mup1 | 6 | 1.00 | 0.82 | 0.96 | 0.97 | 1.00 | +| fragments | Hsp90 2Rings | 6 | 0.73 | 1.33 | 1.47 | 0.43 | 0.83 | +| fragments | Mcl1 | 12 | 0.18 | 0.76 | 0.93 | 0.21 | 0.24 | +| fragments | Jak2 Set1 | 10 | 0.64 | 0.54 | 0.72 | 0.76 | 0.77 | +| fragments | P38 | 6 | 0.60 | 1.10 | 1.37 | 0.83 | 0.77 | +| fragments | T4 Lysozyme | 12 | 0.55 | 0.79 | 0.96 | 0.62 | 0.72 | +| fragments | Jak2 Set2 | 8 | 0.57 | 1.96 | 2.38 | 0.51 | 0.76 | +| fragments | Liga | 11 | 0.78 | 1.64 | 2.09 | 0.94 | 0.90 | diff --git a/summaries/2026_june_08/bayer_macrocycles/brd4/README.md b/summaries/2026_june_08/bayer_macrocycles/brd4/README.md new file mode 100644 index 0000000..68cd070 --- /dev/null +++ b/summaries/2026_june_08/bayer_macrocycles/brd4/README.md @@ -0,0 +1,40 @@ +# Brd4 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.55 +- RMSE: 0.66 +- R²: 0.89 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 2055 +- Map Details: + - Edges: 3 + - Min Dummy Atoms: 8 + - Max Dummy Atoms: 47 + - Mean Dummy Atoms: 29.3 + - Median Dummy Atoms: 33.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.50 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 605.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/bayer_macrocycles/brd4/ddg_results.csv b/summaries/2026_june_08/bayer_macrocycles/brd4/ddg_results.csv new file mode 100644 index 0000000..a6c842b --- /dev/null +++ b/summaries/2026_june_08/bayer_macrocycles/brd4/ddg_results.csv @@ -0,0 +1,4 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +25e,11,65.09205567169391,0.08711500029188558,62.68960798053202,0.08959048103771447,3.1000000000000014,2.4024476911618935,0.12496190446861917,2.3544710628364527,0.0753072568388216 +61a,11,51.771121043854265,0.09420017741519852,47.15837820149695,0.0974022725883792,3.8000000000000007,4.612742842357308,0.13550231042471492,4.669154369060836,0.07254069942294414 +61a,25e,-22.06860334475711,0.062288834535805894,-24.408178977041924,0.06497752310512511,0.6999999999999993,2.3395756322848142,0.09001098497797963,2.3146833062243832,0.06756915264354413 diff --git a/summaries/2026_june_08/bayer_macrocycles/brd4/dg_comparison_plot.png b/summaries/2026_june_08/bayer_macrocycles/brd4/dg_comparison_plot.png new file mode 100644 index 0000000..e05a89b Binary files /dev/null and b/summaries/2026_june_08/bayer_macrocycles/brd4/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/bayer_macrocycles/brd4/dg_plot.png b/summaries/2026_june_08/bayer_macrocycles/brd4/dg_plot.png new file mode 100644 index 0000000..778ed96 Binary files /dev/null and b/summaries/2026_june_08/bayer_macrocycles/brd4/dg_plot.png differ diff --git a/summaries/2026_june_08/bayer_macrocycles/brd4/dg_results.csv b/summaries/2026_june_08/bayer_macrocycles/brd4/dg_results.csv new file mode 100644 index 0000000..c6abc71 --- /dev/null +++ b/summaries/2026_june_08/bayer_macrocycles/brd4/dg_results.csv @@ -0,0 +1,4 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +25e,CCOc1cc(=O)n(C)cc1-c1cc(NS(=O)(=O)CC)ccc1Oc1ccc(F)cc1F,-10.513262585537356,0.04987293980098266,-11.3 +11,COc1cc(=O)n(C)nc1-c1ccccc1Oc1ccccc1,-8.158791522700904,0.05642581685891488,-8.2 +61a,CCS(=O)(=O)Nc1ccc2c(c1)-c1cn(C)c(=O)cc1OCCCCc1cc(F)cc(F)c1O2,-12.82794589176174,0.04558815925845357,-12.0 diff --git a/summaries/2026_june_08/bayer_macrocycles/ftase/README.md b/summaries/2026_june_08/bayer_macrocycles/ftase/README.md new file mode 100644 index 0000000..5140932 --- /dev/null +++ b/summaries/2026_june_08/bayer_macrocycles/ftase/README.md @@ -0,0 +1,40 @@ +# Ftase Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.94 +- RMSE: 0.98 +- R²: 0.22 +- Kendall 𝜏: 0.40 +- Spearman ρ: 0.50 + +## System Details +- Ligands: 5 +- Host Atoms: 13188 +- Map Details: + - Edges: 8 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 58 + - Mean Dummy Atoms: 36.6 + - Median Dummy Atoms: 39.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 3.54 Hours +- Average Time Per Edge: 0.44 Hours +- Total Nanoseconds Simulated: 1513.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/bayer_macrocycles/ftase/ddg_results.csv b/summaries/2026_june_08/bayer_macrocycles/ftase/ddg_results.csv new file mode 100644 index 0000000..05e8617 --- /dev/null +++ b/summaries/2026_june_08/bayer_macrocycles/ftase/ddg_results.csv @@ -0,0 +1,9 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +"lig 2, deprot",lig 49 stereo,5.764328191077008,0.09245334168085052,1.7150371462211504,0.0908721070478824,0.8100000000000005,4.049291044855857,0.1296354898447099,3.190374661813207,0.07516319565388352 +"lig 2, deprot",lig 51 stereo,17.595533057282708,0.09431687345924944,16.76307911905845,0.09264269860252268,1.0099999999999998,0.8324539382242587,0.1322056815098577,1.1852365001458285,0.07380027240098457 +"lig 2, deprot","lig 66, deprot",16.69637950398279,0.09142193866146102,15.099012721902232,0.09190342274791857,0.120000000000001,1.597366782080556,0.1296310533066926,2.1170484881886704,0.07692507158109016 +lig 51 stereo,lig 49 stereo,-11.23778266156757,0.04902303942583153,-13.063222152747365,0.05273488459738261,-0.1999999999999993,1.8254394911797946,0.0720015725387015,2.0051381616673787,0.056845032061041315 +"lig 66, deprot",lig 49 stereo,-7.681505018005634,0.08441806943911394,-8.050834529334457,0.08200152409017783,0.6899999999999995,0.369329511328823,0.11768882870068458,1.0733261736245368,0.060846890646253524 +"lig 66, deprot","lig 68, deprot",9.860684925274699,0.054232776464812255,11.05889442945298,0.052402509143906345,0.17999999999999972,-1.198209504178281,0.07541363940070445,-1.3113963562738693,0.06334077033588915 +"lig 68, deprot",lig 49 stereo,-15.930017216756259,0.0863682721081385,-18.821141824516467,0.08526329918998542,0.5099999999999998,2.8911246077602084,0.12136436303835826,2.384722529898406,0.0611889902669752 +"lig 68, deprot",lig 51 stereo,-4.1950457500431755,0.08834943914564383,-4.352412937233825,0.08684671986978922,0.7099999999999991,0.15736718719064965,0.12388694906846105,0.37958436823102737,0.05950686309533998 diff --git a/summaries/2026_june_08/bayer_macrocycles/ftase/dg_comparison_plot.png b/summaries/2026_june_08/bayer_macrocycles/ftase/dg_comparison_plot.png new file mode 100644 index 0000000..277eac4 Binary files /dev/null and b/summaries/2026_june_08/bayer_macrocycles/ftase/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/bayer_macrocycles/ftase/dg_plot.png b/summaries/2026_june_08/bayer_macrocycles/ftase/dg_plot.png new file mode 100644 index 0000000..7578ca8 Binary files /dev/null and b/summaries/2026_june_08/bayer_macrocycles/ftase/dg_plot.png differ diff --git a/summaries/2026_june_08/bayer_macrocycles/ftase/dg_results.csv b/summaries/2026_june_08/bayer_macrocycles/ftase/dg_results.csv new file mode 100644 index 0000000..c78529d --- /dev/null +++ b/summaries/2026_june_08/bayer_macrocycles/ftase/dg_results.csv @@ -0,0 +1,6 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +"lig 2, deprot",N#Cc1ccc(Cn2cncc2CN2CCN(c3cccc(Cl)c3)C(=O)C2)cc1,-13.421662356412503,0.06270816740003922,-12.41 +lig 49 stereo,N#Cc1ccc2cc1Oc1ccc3cccc(c3c1)N1CC[C@H](NCc3cncn3C2)C1=O,-10.231287694599295,0.04143901208079932,-11.6 +lig 51 stereo,CN1Cc2cncn2Cc2ccc(C#N)c(c2)Oc2ccc3cccc(c3c2)N2CC[C@H]1C2=O,-12.236425856266674,0.03891228530667638,-11.4 +"lig 66, deprot",N#Cc1ccc2cc1Oc1ccc3cccc(c3c1)N1CC[C@H](NCCc3cncn3C2)C1=O,-11.304613868223832,0.044555048861879866,-12.29 +"lig 68, deprot",CN1CCc2cncn2Cc2ccc(C#N)c(c2)Oc2ccc3cccc(c3c2)N2CC[C@H]1C2=O,-12.616010224497701,0.04502111513122874,-12.11 diff --git a/summaries/2026_june_08/dg_plot.png b/summaries/2026_june_08/dg_plot.png new file mode 100644 index 0000000..6a870a1 Binary files /dev/null and b/summaries/2026_june_08/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/hsp90_2rings/README.md b/summaries/2026_june_08/fragments/hsp90_2rings/README.md new file mode 100644 index 0000000..7b77c83 --- /dev/null +++ b/summaries/2026_june_08/fragments/hsp90_2rings/README.md @@ -0,0 +1,40 @@ +# Hsp90 2Rings Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.33 +- RMSE: 1.47 +- R²: 0.43 +- Kendall 𝜏: 0.73 +- Spearman ρ: 0.83 + +## System Details +- Ligands: 6 +- Host Atoms: 3795 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 6 + - Mean Dummy Atoms: 3.3 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.61 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 720.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/hsp90_2rings/ddg_results.csv b/summaries/2026_june_08/fragments/hsp90_2rings/ddg_results.csv new file mode 100644 index 0000000..c28a853 --- /dev/null +++ b/summaries/2026_june_08/fragments/hsp90_2rings/ddg_results.csv @@ -0,0 +1,10 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +15,14,-4.619227091875192,0.047225818131352876,-5.8375915326680845,0.0473894790814662,1.1600000000000001,1.2183644407928915,0.06690321835149891,1.1039049417424307,0.04936632966725383 +14,16,-9.206210689290423,0.051304991717911926,-10.639848619008786,0.05490562775500082,0.6000000000000014,1.4336379297183635,0.07514539330089189,1.341694979595271,0.04987448562479691 +17,16,-3.0107321499110355,0.03980674529514113,-5.868847202808255,0.043335319747861506,1.8000000000000007,2.8581150528972197,0.05884324012698175,2.836278841263268,0.04661676708194859 +17,14,6.2045095449023675,0.05296663066332629,4.763707868984378,0.05462767890031872,1.1999999999999993,1.4408016759179896,0.07608973167163585,1.494583861667997,0.047673280390838915 +17,19,-2.7877867733421944,0.040404330917765706,-0.41732724923729614,0.03903745972767,-0.33999999999999986,-2.3704595241048985,0.05618214323877094,-2.3798749549516955,0.04109900162350875 +18,15,3.952112975143815,0.04026252259289224,1.296587698246239,0.041687157253171965,-0.9199999999999999,2.6555252768975763,0.057955929855312005,2.5152570784210653,0.04508247303656 +18,19,-10.186637502893635,0.03786606923307111,-9.87560753116087,0.03838263542810388,-1.299999999999999,-0.31102997173276453,0.0539172134069489,-0.2552967964561965,0.03998579932789611 +18,16,-10.580400715877087,0.04382662325041237,-15.444947949312692,0.04840310161655989,0.8400000000000016,4.864547233435605,0.0652965018330738,4.960856999758767,0.04563835214613087 +19,15,13.700873976471343,0.04630547518007192,11.002671345206002,0.04821876328573498,0.379999999999999,2.6982026312653407,0.06685242078233218,2.770553874877262,0.04305137368356105 diff --git a/summaries/2026_june_08/fragments/hsp90_2rings/dg_comparison_plot.png b/summaries/2026_june_08/fragments/hsp90_2rings/dg_comparison_plot.png new file mode 100644 index 0000000..2f763ae Binary files /dev/null and b/summaries/2026_june_08/fragments/hsp90_2rings/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/hsp90_2rings/dg_plot.png b/summaries/2026_june_08/fragments/hsp90_2rings/dg_plot.png new file mode 100644 index 0000000..fcd1b2c Binary files /dev/null and b/summaries/2026_june_08/fragments/hsp90_2rings/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/hsp90_2rings/dg_results.csv b/summaries/2026_june_08/fragments/hsp90_2rings/dg_results.csv new file mode 100644 index 0000000..670b827 --- /dev/null +++ b/summaries/2026_june_08/fragments/hsp90_2rings/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +15,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1ccccc1)C2,-8.955502498309372,0.03381557335934877,-9.88 +14,Nc1ncc2c(n1)C[C@H](c1ccccc1-c1ccccc1)C/C2=N\O,-7.851597556566941,0.035965838002116494,-8.72 +16,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1ccncc1)C2,-6.50990257697167,0.03455318817625353,-8.12 +17,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1cccnc1)C2,-9.346181418234938,0.03129217410198689,-9.92 +19,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1-c1cccnc1)C2,-11.726056373186633,0.026644469865623435,-10.26 +18,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1-c1ccccc1)C2,-11.470759576730437,0.02981503603000777,-8.96 diff --git a/summaries/2026_june_08/fragments/hsp90_single_ring/README.md b/summaries/2026_june_08/fragments/hsp90_single_ring/README.md new file mode 100644 index 0000000..0c6dea5 --- /dev/null +++ b/summaries/2026_june_08/fragments/hsp90_single_ring/README.md @@ -0,0 +1,40 @@ +# Hsp90 Single Ring Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.77 +- RMSE: 0.94 +- R²: 0.39 +- Kendall 𝜏: 0.49 +- Spearman ρ: 0.63 + +## System Details +- Ligands: 7 +- Host Atoms: 3795 +- Map Details: + - Edges: 11 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 5 + - Mean Dummy Atoms: 3.4 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.73 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 907.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/hsp90_single_ring/ddg_results.csv b/summaries/2026_june_08/fragments/hsp90_single_ring/ddg_results.csv new file mode 100644 index 0000000..0cc35a4 --- /dev/null +++ b/summaries/2026_june_08/fragments/hsp90_single_ring/ddg_results.csv @@ -0,0 +1,12 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,3,2.582839202470162,0.04061238664650558,0.8526933114418969,0.040277819024084636,0.0,1.7301458910282648,0.057198502204709685,1.4451143462194356,0.048446410940078406 +10,12,10.468213692552125,0.048804607070191575,10.405369753483459,0.045823733181244254,-0.27999999999999936,0.06284393906866584,0.06694553154573991,0.2716762591259023,0.04722512583705337 +10,9,-2.9059662710123426,0.04542655105217846,-4.095928024353846,0.04788865921956056,0.9500000000000002,1.189961753341503,0.06600678163903599,1.366522845445317,0.05191571811057148 +11,12,4.732467127405716,0.04996666010838553,5.872716744594642,0.04805418966991159,-0.47000000000000064,-1.1402496171889271,0.06932439878728675,-1.2474077841196536,0.04300431949313861 +11,2,-6.789091690051441,0.0527059253048489,-7.929850704085222,0.051680847544599555,1.1899999999999995,1.1407590140337813,0.07381615382264545,1.6145854775699258,0.0469125121349964 +3,12,8.57102358259717,0.05095337852951381,9.615304684868953,0.052144130443886876,-0.27999999999999936,-1.0442811022717815,0.07290580994215076,-1.1734380870935333,0.04504628671288877 +3,2,-2.2651346155533445,0.04994542960126793,-4.249342957446693,0.04702838291720601,1.3800000000000008,1.9842083418933483,0.068601856664835,1.688555174596046,0.04879119025365155 +8,11,-2.69454578939336,0.03800899527218823,-0.8376928651745156,0.03937559960337026,-0.08999999999999986,-1.8568529242188447,0.05472770382289174,-1.7728150543884054,0.04531339562480224 +8,2,-8.763778887425387,0.047676586262556456,-8.705477551849743,0.043207594569655276,1.0999999999999996,-0.05830133557564453,0.06434246736135234,-0.1582295768184796,0.049675651497494255 +9,11,8.570453304585097,0.046078104666291274,8.568458463268831,0.044611836878211845,-0.7599999999999989,0.0019948413162671945,0.06413585361781564,0.1525611978002388,0.04810821937755269 +9,8,11.244966148659904,0.052831853074926445,9.340797383471443,0.0511651696539534,-0.669999999999999,1.9041687651884598,0.07354644304824298,1.9253762521886442,0.050806370944627165 diff --git a/summaries/2026_june_08/fragments/hsp90_single_ring/dg_comparison_plot.png b/summaries/2026_june_08/fragments/hsp90_single_ring/dg_comparison_plot.png new file mode 100644 index 0000000..f56acfa Binary files /dev/null and b/summaries/2026_june_08/fragments/hsp90_single_ring/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/hsp90_single_ring/dg_plot.png b/summaries/2026_june_08/fragments/hsp90_single_ring/dg_plot.png new file mode 100644 index 0000000..25aad72 Binary files /dev/null and b/summaries/2026_june_08/fragments/hsp90_single_ring/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/hsp90_single_ring/dg_results.csv b/summaries/2026_june_08/fragments/hsp90_single_ring/dg_results.csv new file mode 100644 index 0000000..8c1208b --- /dev/null +++ b/summaries/2026_june_08/fragments/hsp90_single_ring/dg_results.csv @@ -0,0 +1,8 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,Cc1nc(N)nc2c1C(=O)C[C@@H](c1ccc(F)cc1)C2,-9.525423730355092,0.035693832076989826,-8.31 +3,Cc1nc(N)nc2c1C(=O)C[C@@H](c1ccccc1)C2,-8.080309384135656,0.03275675632040818,-8.31 +12,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1)C2,-9.25374747122919,0.030921883221841102,-8.59 +9,Nc1ncc2c(n1)C[C@H](c1ccc(F)cc1)CC2=O,-8.158900884909775,0.03769870208105277,-7.36 +11,Nc1ncc2c(n1)C[C@H](c1ccc(F)cc1)C/C2=N\O,-8.006339687109536,0.029886596211056948,-8.12 +2,Nc1ncc2c(n1)C[C@H](c1ccccc1)CC2=O,-6.39175420953961,0.03616040876059645,-6.93 +8,Nc1ncc2c(n1)C[C@H](c1ccccc1)C/C2=N\O,-6.233524632721131,0.0340601701400196,-8.03 diff --git a/summaries/2026_june_08/fragments/jak2_set1/README.md b/summaries/2026_june_08/fragments/jak2_set1/README.md new file mode 100644 index 0000000..9e074fa --- /dev/null +++ b/summaries/2026_june_08/fragments/jak2_set1/README.md @@ -0,0 +1,40 @@ +# Jak2 Set1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.54 +- RMSE: 0.72 +- R²: 0.76 +- Kendall 𝜏: 0.64 +- Spearman ρ: 0.77 + +## System Details +- Ligands: 10 +- Host Atoms: 5622 +- Map Details: + - Edges: 17 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 7.0 + - Median Dummy Atoms: 8.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.70 Hours +- Average Time Per Edge: 0.10 Hours +- Total Nanoseconds Simulated: 1927.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/jak2_set1/ddg_results.csv b/summaries/2026_june_08/fragments/jak2_set1/ddg_results.csv new file mode 100644 index 0000000..f334689 --- /dev/null +++ b/summaries/2026_june_08/fragments/jak2_set1/ddg_results.csv @@ -0,0 +1,18 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,1_3E62,-3.6966715214334305,0.06255926008800307,-4.2506352376667005,0.060321200696355215,1.1572899999999997,0.5539637162332698,0.08690401760683092,0.174746781221363,0.05617179366736894 +1_3E62,7,-3.456040042990575,0.06079383967173422,-0.5618480351141323,0.0582295319867067,-2.8738900000000003,-2.894192007876442,0.08418176368681891,-2.6814741406659435,0.06794465208777692 +2_3E63,3,4.32408254674831,0.055297514746141696,0.5498132279187178,0.056475981989407356,2.6713899999999997,3.7742693188295924,0.07904019027537587,3.843001462529954,0.07105188308322824 +2_3E63,8,2.63780702495873,0.04395982652232771,3.3630172649689563,0.0436842929128243,-0.8675499999999996,-0.7252102400102258,0.06197405743669344,-0.6113872642796272,0.06504339867085532 +2_3E63,9,-0.575882302148185,0.044163624987197496,-0.33407573152837416,0.04151177584699519,-0.45687000000000033,-0.24180657061981092,0.060610669902097174,-0.3910933921380364,0.06144255260173745 +4a,6,-0.4932729747566295,0.05739254814723798,-2.7601538743707126,0.05596324943903115,0.6655899999999999,2.266880899614083,0.0801610246354689,2.223348434206059,0.07495223629406227 +4a,7,-11.136034157117058,0.06686237000045671,-10.794832480707473,0.06529032981825082,-1.9963500000000005,-0.34120167640958377,0.09345268155518034,-0.6356756202105291,0.07634115250024613 +5,10,2.2323523326383428,0.05334578670981195,0.48241235565562557,0.05144571229469134,0.6458200000000005,1.749939976982717,0.07411095919765784,1.8168491286697552,0.04981700622023279 +5,1_3E62,-2.607945980491302,0.061230657480915635,-3.9357218171996924,0.059743380333142804,1.8031100000000002,1.3277758367083907,0.0855480269157376,1.9915959098911182,0.051383094918670796 +5,3,21.21147114974516,0.059923869662027215,16.581533856010367,0.061095319432234674,2.5541800000000006,4.629937293734796,0.0855774982796203,4.445871618064912,0.06151147359180428 +5,4a,4.345813593579425,0.06912008298004833,4.01475552517071,0.06882385247712065,0.9255700000000004,0.33105806840871554,0.09754131709671154,-0.054202610564296094,0.06206221282840244 +6,1_3E62,-1.889966609696471,0.05776734805005349,-1.7811421328212311,0.05677483493998241,0.21194999999999986,-0.10882447687523988,0.08099659488644116,-0.17754991375064488,0.06638028252232855 +6,7,-11.294208957468298,0.06146764835866912,-8.407142020314058,0.06163347746040475,-2.6619400000000004,-2.88706693715424,0.08704571981784756,-2.8590240544165884,0.07555831467541688 +8,3,1.4916001338822313,0.062038248102057894,-2.8532952633228374,0.062444393381814754,3.5389399999999993,4.344895397205069,0.08802298843140535,4.454388726809581,0.06915858760483172 +8,5,-19.485228873153627,0.04923179087577608,-19.316885350927873,0.048195637247081195,0.9847599999999987,-0.16834352222575208,0.06889549101710785,0.0085171087446696,0.05446039849669045 +9,10,-13.305469136713617,0.038711164126303245,-15.098071097028848,0.038820242132150025,1.2199,1.7926019603152312,0.05482303737674832,1.605072365272834,0.05500478637689735 +9,8,3.354212377362411,0.05302273006682445,3.695158817426892,0.05228824182679615,-0.41067999999999927,-0.34094644006448105,0.0744679134733668,-0.2202938721415908,0.05924295249259378 diff --git a/summaries/2026_june_08/fragments/jak2_set1/dg_comparison_plot.png b/summaries/2026_june_08/fragments/jak2_set1/dg_comparison_plot.png new file mode 100644 index 0000000..755c6da Binary files /dev/null and b/summaries/2026_june_08/fragments/jak2_set1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/jak2_set1/dg_plot.png b/summaries/2026_june_08/fragments/jak2_set1/dg_plot.png new file mode 100644 index 0000000..26480fb Binary files /dev/null and b/summaries/2026_june_08/fragments/jak2_set1/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/jak2_set1/dg_results.csv b/summaries/2026_june_08/fragments/jak2_set1/dg_results.csv new file mode 100644 index 0000000..ce4c468 --- /dev/null +++ b/summaries/2026_june_08/fragments/jak2_set1/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,Nc1n[nH]c2ccc(-c3cccc(Cl)n3)cc12,-6.544201016241809,0.03870905623452378,-7.14398 +1_3E62,Nc1n[nH]c2ccc(Br)cc12,-6.369454235020446,0.040704783124860706,-5.98669 +7,Cc1nc(C)c(-c2ccc3[nH]nc(N)c3c2)s1,-9.05092837568639,0.05440217254933027,-8.86058 +2_3E63,Nc1n[nH]c2ccc(-c3ccccc3)cc12,-7.758179989376607,0.0474136244176364,-7.90701 +3,Nc1n[nH]c2cc(-c3ccccc3)ccc12,-3.9151785268466526,0.0529180338755707,-5.23562 +8,Nc1n[nH]c2ccc(-c3ccccc3Cl)cc12,-8.369567253656234,0.044526306047539314,-8.77456 +9,Nc1n[nH]c2ccc(-c3cccc(Cl)c3)cc12,-8.149273381514643,0.03907858095940265,-8.36388 +4a,Nc1n[nH]c2ccc(-c3ccn[nH]3)cc12,-8.41525275547586,0.053557214145049895,-6.86423 +6,Cc1noc(C)c1-c1ccc2[nH]nc(N)c2c1,-6.191904321269801,0.05243531766378662,-6.19864 +5,Nc1n[nH]c2ccc(-c3ccncc3)cc12,-8.361050144911564,0.03135830151936147,-7.7898000000000005 diff --git a/summaries/2026_june_08/fragments/jak2_set2/README.md b/summaries/2026_june_08/fragments/jak2_set2/README.md new file mode 100644 index 0000000..2dc74e1 --- /dev/null +++ b/summaries/2026_june_08/fragments/jak2_set2/README.md @@ -0,0 +1,40 @@ +# Jak2 Set2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.96 +- RMSE: 2.38 +- R²: 0.51 +- Kendall 𝜏: 0.57 +- Spearman ρ: 0.76 + +## System Details +- Ligands: 8 +- Host Atoms: 5857 +- Map Details: + - Edges: 12 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 38 + - Mean Dummy Atoms: 19.1 + - Median Dummy Atoms: 21.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.68 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 1782.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/jak2_set2/ddg_results.csv b/summaries/2026_june_08/fragments/jak2_set2/ddg_results.csv new file mode 100644 index 0000000..f088fb9 --- /dev/null +++ b/summaries/2026_june_08/fragments/jak2_set2/ddg_results.csv @@ -0,0 +1,13 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +13_3E64,12,4.9741105878769805,0.08186886557546384,-1.3607360936759163,0.08003032829694424,2.26211,6.334846681552897,0.11448739929760848,6.58023034475282,0.07420052375531506 +13_3E64,15,16.579706793984716,0.0810269366703101,13.638464395849773,0.07949646079319872,2.3178199999999993,2.9412423981349423,0.11351234181717434,3.6949144536444836,0.0770535625727811 +13_3E64,21,-0.3845678261390191,0.043557529029360095,0.14293961957159182,0.04504563930305046,1.3566000000000003,-0.5275074457106109,0.06266073695197073,-0.8306741812545013,0.060806347542734 +14,12,-29.080977676098843,0.08138507597074529,-31.32136329315067,0.07744474822824864,0.3549700000000007,2.240385617051827,0.11234420153662049,2.1598711811929423,0.07885419755830411 +14,15,-10.821865099533763,0.07547567853046286,-10.154291174594386,0.07231304584558873,0.41068000000000016,-0.6675739249393781,0.1045263347157069,-0.7254447099153944,0.0815445783124695 +18,12,-7.76866549184915,0.07821879744575362,-12.856619449057197,0.0757236308277279,0.8903099999999995,5.087953957208046,0.10886803267990956,4.9416763254079346,0.0774465057042737 +18,15,6.405739975630992,0.08418635023473763,3.6326050952315985,0.07991913627590753,0.946019999999999,2.7731348803993936,0.11607932593245443,2.056360434299598,0.0801841320050078 +18,22-flip,-18.553606939285874,0.06504839204804512,-14.269468960988423,0.06527246767901156,-1.7824600000000004,-4.28413797829745,0.09215089985965297,-3.7276116455337824,0.07034270979071516 +20,14,27.65357247292389,0.07165935951622351,21.4397679134407,0.07131737582793099,0.2778699999999992,6.213804559483191,0.10110010831476754,6.094461224592475,0.06991567834274692 +20,22-flip,0.3625295841445465,0.052104786758476004,0.569666186302443,0.05410274992667066,-2.03993,-0.20713660215789656,0.07511335668690435,-0.4149555651562995,0.06716112535260871 +21,20,-1.0122036153679919,0.03420741495303307,-0.2794298089777465,0.03333018003039938,0.27266999999999975,-0.7327738063902455,0.047760319708182696,-0.8434278797780959,0.06125500273165305 +21,22-flip,-0.3865334692063813,0.054435931046326824,0.6952270026221601,0.056482140612864495,-1.7672600000000003,-1.0817604718285414,0.07844426554625804,-1.2583834449343954,0.06349876635802541 diff --git a/summaries/2026_june_08/fragments/jak2_set2/dg_comparison_plot.png b/summaries/2026_june_08/fragments/jak2_set2/dg_comparison_plot.png new file mode 100644 index 0000000..8a55ee8 Binary files /dev/null and b/summaries/2026_june_08/fragments/jak2_set2/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/jak2_set2/dg_plot.png b/summaries/2026_june_08/fragments/jak2_set2/dg_plot.png new file mode 100644 index 0000000..59d1474 Binary files /dev/null and b/summaries/2026_june_08/fragments/jak2_set2/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/jak2_set2/dg_results.csv b/summaries/2026_june_08/fragments/jak2_set2/dg_results.csv new file mode 100644 index 0000000..876c663 --- /dev/null +++ b/summaries/2026_june_08/fragments/jak2_set2/dg_results.csv @@ -0,0 +1,9 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +13_3E64,CC(C)(C)NS(=O)(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-9.860208014103259,0.04539367727425486,-9.69694 +12,CC(C)(C)NS(=O)(=O)c1cccc(-c2ccc3[nH]nc(N)c3c2)c1,-3.2799776693504388,0.058695245029592245,-7.43483 +15,CC(C)(C)NC(=O)Nc1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-6.1652935604587755,0.06226287472224754,-7.37912 +21,Cc1cc(-c2ccc(S(=O)(=O)NC(C)(C)C)cc2)cc2c(N)n[nH]c12,-10.69088219535776,0.040457705879208605,-8.34034 +14,CC(C)(C)NC(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-5.439848850543381,0.05265788339346902,-7.7898000000000005 +18,CCS(=O)(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-8.221653994758373,0.05052553272077619,-8.32514 +22-flip,CC(C)(C)NS(=O)(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)c(Cl)c1,-11.949265640292156,0.04894146875587767,-10.1076 +20,CC(C)(C)NS(=O)(=O)c1ccc(-c2cc(Cl)c3[nH]nc(N)c3c2)cc1,-11.534310075135856,0.04599292765900287,-8.06767 diff --git a/summaries/2026_june_08/fragments/liga/README.md b/summaries/2026_june_08/fragments/liga/README.md new file mode 100644 index 0000000..0e3f998 --- /dev/null +++ b/summaries/2026_june_08/fragments/liga/README.md @@ -0,0 +1,40 @@ +# Liga Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.64 +- RMSE: 2.09 +- R²: 0.94 +- Kendall 𝜏: 0.78 +- Spearman ρ: 0.90 + +## System Details +- Ligands: 11 +- Host Atoms: 5824 +- Map Details: + - Edges: 18 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 20 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.05 Hours +- Average Time Per Edge: 0.11 Hours +- Total Nanoseconds Simulated: 1995.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/liga/ddg_results.csv b/summaries/2026_june_08/fragments/liga/ddg_results.csv new file mode 100644 index 0000000..e8ea601 --- /dev/null +++ b/summaries/2026_june_08/fragments/liga/ddg_results.csv @@ -0,0 +1,19 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,3,8.351694714555046,0.045201586938231134,5.576791041698599,0.047025780784978294,0.5099999999999998,2.7749036728564467,0.0652273525460853,3.042359095090232,0.052200988085293346 +10,13,-42.612102157630794,0.07556880673258622,-34.19964789282328,0.07757245139438236,-4.13,-8.412454264807511,0.10829649009234224,-7.659865456235422,0.06861814931117007 +10,8,48.77177020957925,0.06608477369624607,47.76737569232186,0.06617785959011277,0.71,1.0043945172573838,0.09352382805687938,0.9710702210267499,0.0694026418346556 +11,13,-67.58564775785787,0.06230528402346865,-63.836374622215764,0.06232182045537563,-1.5899999999999999,-3.7492731356421043,0.08812467147239288,-4.070382745342439,0.0823402863013579 +12,10,-11.267068449268308,0.07521657190214154,-16.66169617030558,0.07330492404803399,2.5100000000000007,5.39462772103727,0.10502925582140463,6.269790459608131,0.07355999123415419 +12,11,16.179789971476627,0.06277489932901813,13.074263797909312,0.05986133777026372,-0.02999999999999936,3.105526173567315,0.08674138427194925,2.6803077487151477,0.0865017031258252 +12,13,-52.22985835967813,0.04022254750630529,-50.914884852794515,0.040902482518939756,-1.6199999999999992,-1.3149735068836144,0.05736607363336938,-1.3900749966272912,0.08771921800543891 +3,4,-26.35324984369325,0.03705854894829253,-24.889250326839743,0.03922535496758364,-0.46999999999999975,-1.4639995168535032,0.053962621530888696,-1.2641096146600717,0.049774483023969966 +3,7,-25.152421186090816,0.04265660811449688,-24.72716884647456,0.04359930884588249,0.7800000000000002,-0.4252523396162561,0.060995786310796975,-0.4467634815744512,0.05825274648523203 +5,10,11.551866586710354,0.04985855744655934,16.24458538757152,0.050985964037544865,-1.7400000000000002,-4.692718800861165,0.07131230103908916,-4.469536258637017,0.05661553976948696 +5,4,-5.143042713696005,0.045024384596980244,-2.521719109158443,0.04362727323263115,-1.7000000000000002,-2.6213236045375616,0.06269397242200758,-2.691286778206857,0.05438635257684502 +5,7,-4.4088976596231815,0.045168751393069494,-2.6444002782057283,0.0464237294807783,-0.4500000000000002,-1.7644973814174532,0.06477174354078638,-1.8739406451212366,0.06223952650351812 +6,4,5.299909288466937,0.04911779699933026,5.970697630591465,0.04948284407577697,-1.2000000000000002,-0.670788342124528,0.06972165976147637,-0.7630327584290155,0.05886753623678499 +6,8,72.90268337609811,0.06571438515149972,74.21808453710962,0.06475784906472444,-0.5300000000000002,-1.3154011610115055,0.09226028089773669,-1.570212017832426,0.07813255400422407 +7,4,-0.8878189643714854,0.03638583544832054,-0.16530613646174308,0.04064291580322918,-1.25,-0.7225128279097424,0.05455067026408232,-0.8173461330856204,0.053346572870124134 +9,11,33.008097245693065,0.06689338511806898,36.89959697865611,0.06751824369005863,-2.7,-3.891499732963049,0.09504440122145247,-3.7544979399423015,0.08089484951063901 +9,6,-22.600264056247365,0.04837700432293858,-25.205578511861454,0.04839988393722184,1.08,2.6053144556140886,0.06843159586330105,2.3762670098098573,0.07589778419455262 +9,8,48.96261355750867,0.06764871176101767,48.46707664417269,0.06801029115282965,0.5499999999999998,0.49553691333597644,0.09592574162141207,0.8060549919774314,0.0828514907524645 diff --git a/summaries/2026_june_08/fragments/liga/dg_comparison_plot.png b/summaries/2026_june_08/fragments/liga/dg_comparison_plot.png new file mode 100644 index 0000000..1f9d5d4 Binary files /dev/null and b/summaries/2026_june_08/fragments/liga/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/liga/dg_plot.png b/summaries/2026_june_08/fragments/liga/dg_plot.png new file mode 100644 index 0000000..795e504 Binary files /dev/null and b/summaries/2026_june_08/fragments/liga/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/liga/dg_results.csv b/summaries/2026_june_08/fragments/liga/dg_results.csv new file mode 100644 index 0000000..2a2db0e --- /dev/null +++ b/summaries/2026_june_08/fragments/liga/dg_results.csv @@ -0,0 +1,12 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,FC(F)(F)c1cccc(-c2nc[nH]n2)n1,-6.679451773624717,0.03481997643431966,-6.54 +3,Clc1cncc(-c2nc[nH]n2)n1,-3.6370926785344855,0.038891032362157234,-6.03 +13,OCCNc1cc(C(F)(F)F)nc(-c2n[nH]c3cnccc23)n1,-14.33931722986014,0.059127148214702975,-10.67 +8,c1cc(-c2nc[nH]n2)nc(C2CCC2)c1,-5.7083815525979675,0.060035788782549615,-5.83 +11,FC(F)(F)c1cccc(-c2n[nH]c3cnccc23)n1,-10.2689344845177,0.057305349594833924,-9.08 +12,OCCNc1cc(-c2n[nH]c3cnccc23)nc(C(F)(F)F)c1,-12.949242233232848,0.06479692547862333,-9.05 +4,Clc1cccc(-c2nc[nH]n2)n1,-4.901202293194557,0.03106423606189461,-6.5 +7,Cc1cccc(-c2nc[nH]n2)n1,-4.083856160108937,0.043368999007105884,-5.25 +5,c1ccc(-c2nc[nH]n2)nc1,-2.2099155149877,0.044641780704893295,-4.8 +6,COc1cccc(-c2nc[nH]n2)n1,-4.138169534765542,0.050004000444765224,-5.3 +9,CC(F)(F)c1cccc(-c2nc[nH]n2)n1,-6.514436544575399,0.05709705408480196,-6.38 diff --git a/summaries/2026_june_08/fragments/mcl1/README.md b/summaries/2026_june_08/fragments/mcl1/README.md new file mode 100644 index 0000000..c259ba8 --- /dev/null +++ b/summaries/2026_june_08/fragments/mcl1/README.md @@ -0,0 +1,40 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.76 +- RMSE: 0.93 +- R²: 0.21 +- Kendall 𝜏: 0.18 +- Spearman ρ: 0.24 + +## System Details +- Ligands: 12 +- Host Atoms: 2428 +- Map Details: + - Edges: 20 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 19 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.58 Hours +- Average Time Per Edge: 0.08 Hours +- Total Nanoseconds Simulated: 2238.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/mcl1/ddg_results.csv b/summaries/2026_june_08/fragments/mcl1/ddg_results.csv new file mode 100644 index 0000000..eb4cf7c --- /dev/null +++ b/summaries/2026_june_08/fragments/mcl1/ddg_results.csv @@ -0,0 +1,21 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +11,14,-4.669759943712471,0.06335850917930452,-5.646415692732055,0.06575966794762315,-0.0600000000000005,0.9766557490195847,0.09131612461118611,1.1455903182593232,0.07014583383184746 +10,15,-1.3956055308719155,0.06491133803392479,-1.022919789906759,0.06552328267882426,-0.2699999999999996,-0.3726857409651563,0.09223221984948406,-0.5651794368180383,0.07408958910465441 +2,13 flipped,4.158431908140365,0.053986042929741754,2.0643508358984,0.05512526212209996,0.1200000000000001,2.094081072241965,0.07715754891935168,1.8412855739082223,0.054128323829071366 +2,14,2.813775292931619,0.06559526689072884,2.5533684674342787,0.06546051156804489,-0.28000000000000025,0.26040682549734046,0.09267047864997831,0.02512249695612745,0.0578673486137216 +2,3,0.20779444550610623,0.04242416551355929,2.7648983039362363,0.04465329106169464,-1.0599999999999996,-2.5571038584301298,0.06159323195093997,-2.607500692767873,0.055746385052 +2,15,14.019316358536045,0.07248664260078157,15.744083674164658,0.07009315856217385,0.020000000000000462,-1.724767315628612,0.10083334881256045,-1.3618204460331427,0.06334521233913304 +2,4,-5.498989004448693,0.04225875692237055,-4.666027987549903,0.043678458752903916,-0.47999999999999954,-0.8329610168987902,0.06077507956105964,-0.7090643348688701,0.05129965135128416 +2,5,0.3347133864892023,0.04600029587801879,0.46067625312566085,0.0445376120681896,-0.71,-0.12596286663645853,0.0640283227142631,-0.06896114335371628,0.0537642725247353 +3,11,6.262029475221456,0.0630654126881643,5.07268105019062,0.06273832425463025,0.8399999999999999,1.1893484250308357,0.08895697616155576,1.4870328714646774,0.06840663282715366 +3,4,-5.410203844173347,0.05086334086917739,-7.578838708040358,0.05216416319671349,0.5800000000000001,2.1686348638670103,0.07285725335467629,1.8984363578990031,0.06345497547313284 +4,11,12.380358953941053,0.06161380005310334,12.660285419147561,0.061464093445523865,0.2599999999999998,-0.279926465206509,0.08702927748788844,-0.41140348643432567,0.06483411291246668 +5,10,15.414135443760797,0.06117321121173684,15.898686125494756,0.060855603230253956,1.0,-0.4845506817339599,0.08628769445566303,-0.7276798658613881,0.06608515935912299 +5,8,12.072725499967738,0.05649070011186101,13.585305468619303,0.0558848205236005,-0.33000000000000007,-1.5125799686515653,0.07946264760302951,-1.2185959957608068,0.06150654020166029 +7,13 flipped,-10.997908387948952,0.04958276985072196,-12.328389235175823,0.050098002018230524,0.6699999999999999,1.3304808472268723,0.07048589129952385,1.5031181319183862,0.0578694053591869 +7,14,-12.03991819897135,0.05701723783772796,-11.681541608248834,0.055674163429031205,0.2699999999999996,-0.3583765907225155,0.07969051313780401,-0.3130449450337087,0.06138096343055444 +7,8,-1.5523631259795259,0.05322308480885611,-0.1258184729083689,0.05118055773069561,-0.4900000000000002,-1.426544653071157,0.07383865008378578,-1.6257245811043592,0.05499299852143716 +7,9,-0.3297636863114297,0.053171477026066435,0.6469357783304193,0.05157711839745555,0.39999999999999947,-0.976699464641849,0.07407702147979937,-1.006078129863261,0.061812626409534645 +8,10,2.7420880642496828,0.048063366098174486,2.297151589920217,0.04770714586393598,1.33,0.4449364743294654,0.06772044689139323,0.4909161298994187,0.06388965908270593 +9,13 flipped,-10.299218575659964,0.048650093298094416,-12.770286280703106,0.050746511288405564,0.27000000000000046,2.471067705043141,0.07029964427973703,2.5091962617816472,0.06796251779676186 +9,15,-0.11466672930734527,0.060111893408589925,0.4920846344181059,0.05527806268795765,0.17000000000000082,-0.6067513637254511,0.0816645819416193,-0.6939097581597178,0.0755092332832231 diff --git a/summaries/2026_june_08/fragments/mcl1/dg_comparison_plot.png b/summaries/2026_june_08/fragments/mcl1/dg_comparison_plot.png new file mode 100644 index 0000000..c1ee981 Binary files /dev/null and b/summaries/2026_june_08/fragments/mcl1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/mcl1/dg_plot.png b/summaries/2026_june_08/fragments/mcl1/dg_plot.png new file mode 100644 index 0000000..47971d3 Binary files /dev/null and b/summaries/2026_june_08/fragments/mcl1/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/mcl1/dg_results.csv b/summaries/2026_june_08/fragments/mcl1/dg_results.csv new file mode 100644 index 0000000..5b88d28 --- /dev/null +++ b/summaries/2026_june_08/fragments/mcl1/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,O=C([O-])c1cc2c(Br)cc(Cl)cc2o1,-6.254188841163557,0.04927674755703548,-5.55 +14,Cn1c(C(=O)[O-])cc2cc(Br)ccc21,-5.108598522904233,0.04992234123281232,-5.61 +10,Cc1ccc2c(C)c(C(=O)[O-])oc2c1C,-5.930362029075465,0.04830156486930116,-5.04 +15,Cc1cccc2c(-c3ccccc3)c(C(=O)[O-])[nH]c12,-6.495541465893504,0.05618029943737588,-5.31 +2,O=C([O-])c1sc2ccccc2c1Cl,-5.133721019860361,0.02926413985437868,-5.33 +13 flipped,Cn1c(C(=O)[O-])cc2ccccc21,-3.2924354459521386,0.04553554171334937,-5.21 +3,O=C([O-])c1sc2cccc(Cl)c2c1Cl,-7.741221712628234,0.047447545404891225,-6.39 +4,O=C([O-])c1sc2cc(Cl)ccc2c1Cl,-5.842785354729231,0.04213388597490951,-5.81 +5,Cc1ccc2c(Cl)c(C(=O)[O-])sc2c1,-5.202682163214077,0.04510218529846833,-6.04 +8,Cc1c(C(=O)[O-])oc2cc(Cl)ccc12,-6.421278158974884,0.04181922248058996,-6.37 +7,Cc1c(C(=O)[O-])oc2ccc(Cl)cc12,-4.795553577870525,0.035712498057370735,-5.88 +9,Cc1c(C(=O)[O-])oc2c(C)cccc12,-5.801631707733786,0.050452138370409946,-5.48 diff --git a/summaries/2026_june_08/fragments/mup1/README.md b/summaries/2026_june_08/fragments/mup1/README.md new file mode 100644 index 0000000..f48389e --- /dev/null +++ b/summaries/2026_june_08/fragments/mup1/README.md @@ -0,0 +1,40 @@ +# Mup1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.82 +- RMSE: 0.96 +- R²: 0.97 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 6 +- Host Atoms: 2486 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 7.8 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.62 Hours +- Average Time Per Edge: 0.06 Hours +- Total Nanoseconds Simulated: 823.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/mup1/ddg_results.csv b/summaries/2026_june_08/fragments/mup1/ddg_results.csv new file mode 100644 index 0000000..615f204 --- /dev/null +++ b/summaries/2026_june_08/fragments/mup1/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +IBT,PT,-3.8597469453924087,0.042248115335304565,-5.160064675775362,0.04345567480020525,0.8900000000000006,1.300317730382953,0.06060774638382779,1.298349269380184,0.0396662300303278 +IBT,ET,-6.004282953217313,0.04588450746435758,-9.644567320808498,0.04623978648419232,2.13,3.640284367591185,0.0651421973788909,3.646442556900854,0.03841874137183068 +IPT,ET,-2.284501260108812,0.04109121258997573,-4.347994192190903,0.04459796421566731,0.8899999999999997,2.0634929320820916,0.06064211543388407,1.898246251234844,0.04003360858019703 +IBT,SBT_S,0.19013569592037563,0.05541410136929401,0.06740967850080366,0.05669383852697247,0.6699999999999999,0.12272601741957197,0.0792774492367711,0.11697331301588854,0.0462701640432536 +MT,ET,2.54934931616501,0.04096058092653601,4.713151764927268,0.040761785829979594,-1.3200000000000003,-2.163802448762258,0.05778661068005659,-2.141557486056114,0.039588346195243304 +MT,IPT,5.0966397601371645,0.04552778343644482,8.81917196438789,0.04608842853094018,-2.21,-3.722532204250726,0.06478365773161777,-4.039803737290958,0.0438115622121625 +MT,PT,3.8215745901879288,0.041386801211935595,8.578444647626254,0.046513942964471554,-2.5599999999999996,-4.7568700574383245,0.06226085611890015,-4.489650773576784,0.0408000891015902 +PT,IPT,-0.06772121668823425,0.051207835792304646,-0.35088789298718553,0.05304655134321705,0.34999999999999964,0.28316667629895126,0.07373044863514801,0.449847036285826,0.04123226809400242 +PT,SBT_S,4.157590070768519,0.04375509433014256,5.482822804490184,0.04356068217722862,-0.22000000000000064,-1.3252327337216654,0.061741730714203316,-1.1813759563642954,0.044864378912160635 +SBT_S,ET,-6.681922887142295,0.05190653660839213,-10.010117182413438,0.05264836112941673,1.46,3.3281942952711434,0.07393333803022714,3.5294692438849653,0.0437653102234025 diff --git a/summaries/2026_june_08/fragments/mup1/dg_comparison_plot.png b/summaries/2026_june_08/fragments/mup1/dg_comparison_plot.png new file mode 100644 index 0000000..3b46481 Binary files /dev/null and b/summaries/2026_june_08/fragments/mup1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/mup1/dg_plot.png b/summaries/2026_june_08/fragments/mup1/dg_plot.png new file mode 100644 index 0000000..97c79da Binary files /dev/null and b/summaries/2026_june_08/fragments/mup1/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/mup1/dg_results.csv b/summaries/2026_june_08/fragments/mup1/dg_results.csv new file mode 100644 index 0000000..999589d --- /dev/null +++ b/summaries/2026_june_08/fragments/mup1/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +IBT,CC(C)CC1=NCCS1,-9.792993581319983,0.029167836654734554,-9.09 +PT,CCCC1=NCCS1,-8.4946443119398,0.026882096452873653,-8.2 +ET,CCC1=NCCS1,-6.1465510244191295,0.02500473942032465,-6.96 +IPT,CC(C)C1=NCCS1,-8.044797275653973,0.03126424191427145,-7.85 +SBT_S,CC[C@H](C)C1=NCCS1,-9.676020268304095,0.03591887227450664,-8.42 +MT,CC1=NCCS1,-4.004993538363015,0.03069202112921365,-5.64 diff --git a/summaries/2026_june_08/fragments/p38/README.md b/summaries/2026_june_08/fragments/p38/README.md new file mode 100644 index 0000000..44c1c4c --- /dev/null +++ b/summaries/2026_june_08/fragments/p38/README.md @@ -0,0 +1,40 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.10 +- RMSE: 1.37 +- R²: 0.83 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.77 + +## System Details +- Ligands: 6 +- Host Atoms: 7065 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 4 + - Max Dummy Atoms: 32 + - Mean Dummy Atoms: 19.6 + - Median Dummy Atoms: 20.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.62 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 1437.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/p38/ddg_results.csv b/summaries/2026_june_08/fragments/p38/ddg_results.csv new file mode 100644 index 0000000..598896b --- /dev/null +++ b/summaries/2026_june_08/fragments/p38/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +1_1W7H,3,35.82556185516214,0.04752403786067399,34.72302824291051,0.04723015775005596,-0.1499999999999999,1.1025336122516363,0.06700165651443211,0.9476149395291351,0.04808626159957594 +1_1W7H,5_1WBW,7.236994715395616,0.06321265289254045,10.107867891625176,0.06290756448125474,-2.0000000000000004,-2.8708731762295603,0.08918072187797106,-2.923776537861669,0.0567428111555411 +1_1W7H,6,4.292367592291317,0.07168638551057137,8.167264178751644,0.0726369253628795,-1.1,-3.8748965864603266,0.10205420517422487,-3.4462037552183453,0.058498933053639894 +4,3,38.57179245882151,0.05828586716248094,35.29809650623752,0.05888042120393161,1.3100000000000005,3.273695952583992,0.08285014370557707,3.3305451233482204,0.050861857656843444 +4,5_1WBW,10.268389333248782,0.06455420484036604,10.367264674603327,0.06198966689050391,-0.54,-0.09887534135454487,0.08949840313529386,-0.5408463540425839,0.059113337137363095 +4,7,8.555554951880874,0.0706984915203204,12.00915185342601,0.0720045735630507,-0.8999999999999995,-3.453596901545135,0.10091053125043786,-2.976061975088739,0.06561868713539758 +5_1WBW,3,29.454471009201455,0.06933727640288134,24.9973254390259,0.06830844647251558,1.8500000000000005,4.457145570175556,0.09733294282234607,3.8713914773908042,0.054808732372298795 +6,3,30.935417511706486,0.0673530358025943,26.68585374980295,0.06658167505704839,0.9500000000000002,4.24956376190354,0.09470771291308817,4.39381869474748,0.05662486816619636 +6,7,1.4295995892898434,0.07541717056884176,3.628549537097123,0.0756508808459899,-1.2599999999999998,-2.198949947807279,0.10682137140752282,-1.912788403689479,0.07018019116465347 +7,3,28.964825893337423,0.07400574690009465,23.411482746215075,0.07063262617286464,2.21,5.553343147122348,0.10230258283306688,6.3066070984369595,0.06176910731195583 diff --git a/summaries/2026_june_08/fragments/p38/dg_comparison_plot.png b/summaries/2026_june_08/fragments/p38/dg_comparison_plot.png new file mode 100644 index 0000000..21f29e2 Binary files /dev/null and b/summaries/2026_june_08/fragments/p38/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/p38/dg_plot.png b/summaries/2026_june_08/fragments/p38/dg_plot.png new file mode 100644 index 0000000..a9bb183 Binary files /dev/null and b/summaries/2026_june_08/fragments/p38/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/p38/dg_results.csv b/summaries/2026_june_08/fragments/p38/dg_results.csv new file mode 100644 index 0000000..c433a13 --- /dev/null +++ b/summaries/2026_june_08/fragments/p38/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1_1W7H,Nc1ncccc1OCc1ccccc1,-2.924285383953702,0.03555304507491571,-3.94 +3,c1ccc(COc2cccnc2)cc1,-1.9766704444245669,0.0323769909121256,-4.09 +5_1WBW,Nc1ncccc1OCc1cccc2ccccc12,-5.848061921815371,0.0442236091215361,-5.94 +6,OCCNc1ccc(OCc2c(Cl)cccc2Cl)cn1,-6.370489139172047,0.0464554211509836,-5.04 +4,Nc1ncccc1OCc1c(Cl)cccc1Cl,-5.307215567772787,0.03922574440059921,-5.4 +7,CC(C)(CO)Nc1ccc(OCc2c(Cl)cccc2Cl)cn1,-8.283277542861526,0.05260373634630958,-6.3 diff --git a/summaries/2026_june_08/fragments/t4_lysozyme/README.md b/summaries/2026_june_08/fragments/t4_lysozyme/README.md new file mode 100644 index 0000000..65ecccb --- /dev/null +++ b/summaries/2026_june_08/fragments/t4_lysozyme/README.md @@ -0,0 +1,40 @@ +# T4 Lysozyme Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.79 +- RMSE: 0.96 +- R²: 0.62 +- Kendall 𝜏: 0.55 +- Spearman ρ: 0.72 + +## System Details +- Ligands: 12 +- Host Atoms: 2609 +- Map Details: + - Edges: 22 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 6.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.37 Hours +- Average Time Per Edge: 0.06 Hours +- Total Nanoseconds Simulated: 1902.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/fragments/t4_lysozyme/ddg_results.csv b/summaries/2026_june_08/fragments/t4_lysozyme/ddg_results.csv new file mode 100644 index 0000000..5e1aa8a --- /dev/null +++ b/summaries/2026_june_08/fragments/t4_lysozyme/ddg_results.csv @@ -0,0 +1,23 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +butyl benzene,propyl benzene,-4.299001924015287,0.04399773188425293,-3.907489671204348,0.04160106879468862,0.15000000000000036,-0.3915122528109391,0.06055121250494513,-0.3553004734647427,0.05666923393367506 +butyl benzene,isobutyl benzene,-0.0034303846888952875,0.056906092865797044,-0.2554646962664342,0.05354474966181467,0.21999999999999975,0.2520343115775389,0.07813669830237978,0.2248928374250312,0.05824366482915756 +ethyl benzene,benzene,-0.24186892167996812,0.051548472717784705,-2.183237173838351,0.05106650728339236,0.5599999999999996,1.9413682521583826,0.07256054854851193,2.5849268105385623,0.038424680978314446 +ethyl benzene,butyl benzene,6.213974451827791,0.04735114271116022,6.869374961123949,0.0470531061002912,-0.9400000000000004,-0.6554005092961582,0.06675421716819037,-0.6311993025499874,0.0483466560410101 +ethyl benzene,isobutyl benzene,7.061403361112875,0.047283933365389705,7.268987897074818,0.04843462234246172,-0.7200000000000006,-0.20758453596194307,0.06768813039196389,-0.40630646512495616,0.04336426968654525 +ethyl benzene,m-xylene,0.8758623141175647,0.05454251891336753,-2.1303899138201747,0.053073834058053264,1.0,3.0062522279377393,0.07610333915825788,2.807308421062443,0.043688038162719295 +ethyl benzene,o-xylene,1.95333229580299,0.05635985510386742,-1.1035101586871432,0.053272631212394374,1.1499999999999995,3.056842454490133,0.07755260475071553,2.8434484421920665,0.04411462835387955 +ethyl benzene,ortho methyl ethyl benzene,3.9130855076683573,0.04443828169917207,2.2466289880681685,0.04568029612069973,1.1899999999999995,1.666456519600189,0.06372950913077698,1.662136734341379,0.04147872727441637 +ethyl benzene,p-xylene,-1.3146401891364585,0.05405387007175351,-2.3792471588961384,0.05368381382292789,1.0899999999999999,1.0646069697596796,0.07618249625936915,1.2388080611438994,0.04226229030075849 +ethyl benzene,para methyl ethyl benzene,-0.8808489081632412,0.043265843023194625,0.11324413295492614,0.04553861432457586,0.33999999999999986,-0.9940930411181674,0.06281479576588771,-1.1558974006485343,0.0461882223438779 +m-xylene,benzene,0.18967612699368772,0.051947781429394296,-0.4981892543790932,0.05262086894998904,-0.4400000000000004,0.687865381372781,0.0739427335475775,-0.22238161052388072,0.05059215595058722 +meta methyl ethyl benzene,ethyl benzene,-1.951792762186269,0.047474273533330766,-0.39421927518621763,0.046288473140432135,-0.6399999999999997,-1.5575734870000513,0.06630557588310365,-1.5470044038591535,0.04384343761247535 +meta methyl ethyl benzene,ortho methyl ethyl benzene,1.775795224584078,0.05205822103434961,1.7067152295320989,0.05260609333909818,0.5499999999999998,0.06907999505197913,0.07400986038132426,0.1151323304822256,0.053077276634361244 +meta methyl ethyl benzene,para methyl ethyl benzene,-2.935597031994898,0.05271787702662416,-0.29216752369957794,0.05216894761884506,-0.2999999999999998,-2.64342950829532,0.07416720066075075,-2.702901804507688,0.056833655186892554 +methyl benzene,benzene,0.7077640500686371,0.042847239349275784,-0.1227377600814276,0.044775440418475546,0.3200000000000003,0.8305018101500646,0.061973591024908195,1.0004531544518227,0.04188498159121456 +methyl benzene,m-xylene,2.2044597376651387,0.0434703439301818,0.4654157889920179,0.044911895836357574,0.7600000000000007,1.7390439486731208,0.06250399338461606,1.2228347649757034,0.04676045608330141 +methyl benzene,o-xylene,2.675087941051527,0.04508961745782897,1.5304518746677471,0.04506267855874742,0.9100000000000001,1.1446360663837796,0.06374730269887777,1.2589747861053269,0.04715926218053094 +methyl benzene,p-xylene,-0.28335123305974114,0.043776690662843454,0.14861991519748655,0.04518625728034611,0.8500000000000005,-0.43197114825722766,0.06291419944969433,-0.3456655949428402,0.04543123106494834 +methyl benzene,propyl benzene,2.742165729611237,0.046122292944469685,5.473123057862213,0.04570839938526627,-1.0299999999999994,-2.730957328250976,0.06493476480914125,-2.5709734321014697,0.044468337521847076 +ortho methyl ethyl benzene,o-xylene,-2.0323832739902095,0.04375945390749101,-3.1855942778226582,0.043720221608346176,-0.040000000000000036,1.153211003832449,0.06185747799389117,1.1813117078506874,0.05330150755881494 +p-xylene,para methyl ethyl benzene,-0.007244813705576728,0.03969284695020955,2.560240679601717,0.04193745844165232,-0.75,-2.5674854933072937,0.05774315993741661,-2.3947054617924337,0.055623003529917066 +propyl benzene,isobutyl benzene,4.122278376578878,0.04439453343288493,3.723223582078634,0.042628108549442094,0.0699999999999994,0.3990547945002437,0.06154697585768577,0.5801933108897739,0.05248297638024427 diff --git a/summaries/2026_june_08/fragments/t4_lysozyme/dg_comparison_plot.png b/summaries/2026_june_08/fragments/t4_lysozyme/dg_comparison_plot.png new file mode 100644 index 0000000..23ea816 Binary files /dev/null and b/summaries/2026_june_08/fragments/t4_lysozyme/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/fragments/t4_lysozyme/dg_plot.png b/summaries/2026_june_08/fragments/t4_lysozyme/dg_plot.png new file mode 100644 index 0000000..3cd22cf Binary files /dev/null and b/summaries/2026_june_08/fragments/t4_lysozyme/dg_plot.png differ diff --git a/summaries/2026_june_08/fragments/t4_lysozyme/dg_results.csv b/summaries/2026_june_08/fragments/t4_lysozyme/dg_results.csv new file mode 100644 index 0000000..7312361 --- /dev/null +++ b/summaries/2026_june_08/fragments/t4_lysozyme/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +butyl benzene,CCCCc1ccccc1,-6.961882934623825,0.04387062660614478,-6.66 +propyl benzene,CCCc1ccccc1,-7.317183408088567,0.03587157922107431,-6.51 +isobutyl benzene,CC(C)Cc1ccccc1,-6.7369900971987935,0.038310476555577684,-6.44 +ethyl benzene,CCc1ccccc1,-6.330683632073837,0.020316674716398843,-5.72 +benzene,c1ccccc1,-3.745756821535275,0.0326142428511422,-5.16 +m-xylene,Cc1cccc(C)c1,-3.5233752110113943,0.03867657439555962,-4.72 +o-xylene,Cc1ccccc1C,-3.487235189881771,0.03915779824337616,-4.57 +ortho methyl ethyl benzene,CCc1ccccc1C,-4.668546897732458,0.036162377476784524,-4.53 +p-xylene,Cc1ccc(C)cc1,-5.091875570929938,0.03705852007209172,-4.63 +para methyl ethyl benzene,CCc1ccc(C)cc1,-7.486581032722372,0.04147993022843145,-5.38 +meta methyl ethyl benzene,CCc1cccc(C)c1,-4.783679228214684,0.03885202375870603,-5.08 +methyl benzene,Cc1ccccc1,-4.746209975987098,0.02628046510515182,-5.48 diff --git a/summaries/2026_june_08/gpcrs/a2a/README.md b/summaries/2026_june_08/gpcrs/a2a/README.md new file mode 100644 index 0000000..088098b --- /dev/null +++ b/summaries/2026_june_08/gpcrs/a2a/README.md @@ -0,0 +1,40 @@ +# A2A Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.72 +- RMSE: 2.34 +- R²: 0.57 +- Kendall 𝜏: 0.55 +- Spearman ρ: 0.72 + +## System Details +- Ligands: 25 +- Host Atoms: 4651 +- Map Details: + - Edges: 41 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 3.4 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 8.11 Hours +- Average Time Per Edge: 0.20 Hours +- Total Nanoseconds Simulated: 3090.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1ccc_amber14.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/gpcrs/a2a/ddg_results.csv b/summaries/2026_june_08/gpcrs/a2a/ddg_results.csv new file mode 100644 index 0000000..e9854fa --- /dev/null +++ b/summaries/2026_june_08/gpcrs/a2a/ddg_results.csv @@ -0,0 +1,42 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +4a,4a flipped,4.311108936653747,0.05681748111601014,0.008234911479750391,0.05430717548021463,0.0,4.302874025173997,0.07859704491268736,3.2682896207720074,0.07079785981403192 +4a,4b D,-4.733910057249278,0.04187374032019584,-0.8447475489672105,0.04443860764241712,-0.5457000000000001,-3.8891625082820678,0.061058987688954416,-3.8480783884160594,0.06296540325589652 +4a,4b U,-3.890344805271107,0.0415171046325906,-0.8579704492503689,0.043709713104853845,-0.5457000000000001,-3.0323743560207377,0.06028440094072518,-2.463778647316225,0.06548847503192838 +4b D,4a flipped,7.013099000311186,0.05890554445895449,0.8679623127761765,0.05943111882529918,0.5457000000000001,6.145136687535009,0.08367748235237898,7.116368009188067,0.06605682038195874 +4b D,4c,-4.01738955328242,0.041850866079147585,-1.9768740365933573,0.04477212723095534,-1.5007000000000001,-2.040515516689063,0.06128652680940239,-2.34924423428831,0.06045385246768246 +4b D,4e D,-12.774912510926521,0.04617580545544499,-9.290681051888702,0.04501699263239566,-2.114600000000001,-3.4842314590378187,0.06448825191555643,-3.673429484082444,0.06357372109603764 +4b U,4c,-5.998729275834228,0.04347319800909468,-2.010913683195812,0.043014144776244,-1.5007000000000001,-3.9878155926384165,0.06115664801123122,-3.7335439753881445,0.06307746533441369 +4b U,4e U,-13.160648746022856,0.04567527667801075,-9.333874831315429,0.04351694894011352,-2.114600000000001,-3.826773914707427,0.06308689043429927,-3.7895601400768015,0.06667537860712403 +4b U,4m U,-17.548846524196616,0.037567796272291655,-14.410844402212744,0.04023074610627095,-0.5914000000000001,-3.1380021219838725,0.055044093679736845,-2.8982752803123226,0.06539771921837502 +4c,4d,6.986566241390103,0.03926668768258497,5.284277634852758,0.04037908592986084,0.9550000000000001,1.7022886065373448,0.056323559387637744,1.657207369962034,0.060287802692977864 +4d,4f,-13.106348456768485,0.045033747723326766,-9.19109816099744,0.04578237727437944,-0.9413,-3.915250295771045,0.0642188796453337,-3.688057971630787,0.0565099420555529 +4e D,4m D,-3.391437626387944,0.046501284437964197,-5.216240749311036,0.04332175753240232,1.523200000000001,1.8248031229230923,0.06355426130541293,1.7279906796340203,0.0695175013321357 +4e U,4m U,-4.216162846889418,0.04265063661970644,-5.204987952663309,0.04573196374420516,1.523200000000001,0.9888251057738915,0.06253390529918582,0.8912848597644789,0.06898160993920303 +4g,4f,9.770881262901595,0.04254654882508934,10.746224877408853,0.04363916846333018,-0.3819999999999997,-0.9753436145072576,0.060947402250601475,-1.149141025485667,0.05204044757846088 +4g,4i,-6.787582241320369,0.04896104814109344,-6.986017869839447,0.04828548269131245,0.7502999999999993,0.1984356285190786,0.06876534064343391,0.26532118758107437,0.05672144820867557 +4g,4jR,-1.7706269679639597,0.040938382133281666,-2.845979922155288,0.04149529550912084,0.17730000000000068,1.0753529541913283,0.0582907426705121,1.2215735234365361,0.05753895105732917 +4g,4jS,-3.6256994111671514,0.04059667570658925,-2.9273592276799127,0.04319384077482167,0.17730000000000068,-0.6983401834872385,0.05927729716600295,-0.6557470316846068,0.05930832433918414 +4g,4kD,16.598409620003128,0.039606085766556096,16.6830378125238,0.03754375162098691,-0.47749999999999915,-0.08462819252067257,0.054572660880024486,-0.3717568018179822,0.05858211165013539 +4g,4kU,15.009573454618389,0.034303874684155265,16.754606756951226,0.03600217505211379,-0.47749999999999915,-1.7450333023328357,0.04972838652951926,-1.5622884911091361,0.05477518475709336 +4h,4f,12.308837111178265,0.051452826852602884,12.752076682738531,0.05317423590617928,-0.7911999999999999,-0.44323957156026533,0.07399251823887289,-0.4886898942926603,0.06015736564127536 +4h,4lD,17.179469348097427,0.03800526033263612,17.095993708238534,0.03657991199965404,-0.7230000000000008,0.08347563985889399,0.05274931065761787,-0.001594595873948279,0.06891459853519408 +4h,4lU,15.821979400145855,0.040280096891399046,17.11555702259611,0.037089959789857525,-0.7230000000000008,-1.2935776224502569,0.054755377113063,-1.1770244476546026,0.061326703899114016 +4jR,4d,23.402743460119527,0.04777821355877934,22.684346255481714,0.04977715388796222,0.3819999999999997,0.7183972046378146,0.06899654150792052,1.3173434227085838,0.06161084527689206 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b/summaries/2026_june_08/gpcrs/a2a/dg_results.csv @@ -0,0 +1,26 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +4a,Nc1nnc(-c2ccccc2)c(-c2ccccc2)n1,-4.974593520269028,0.04802850946287329,-9.4133 +4a flipped,Nc1nnc(-c2ccccc2)c(-c2ccccc2)n1,-1.706303899497021,0.052015374967619,-9.4133 +4b D,Nc1nnc(-c2cccc(Cl)c2)c(-c2ccccc2)n1,-8.822671908685088,0.04071737081335623,-9.959 +4b U,Nc1nnc(-c2cccc(Cl)c2)c(-c2ccccc2)n1,-7.438372167585253,0.04451968823770217,-9.959 +4c,Nc1nnc(-c2cc(Cl)cc(Cl)c2)c(-c2ccccc2)n1,-11.171916142973398,0.044685165236708735,-11.4597 +4e D,Nc1nnc(-c2ccc(O)c(Cl)c2)c(-c2ccccc2)n1,-12.496101392767532,0.04882329083587491,-12.0736 +4e U,Nc1nnc(-c2ccc(O)c(Cl)c2)c(-c2ccccc2)n1,-11.227932307662055,0.04963470027733758,-12.0736 +4m U,Nc1nnc(-c2ccnc(Cl)c2)c(-c2ccccc2)n1,-10.336647447897576,0.047904687016859,-10.5504 +4d,Cc1cc(C)cc(-c2nnc(N)nc2-c2ccccc2)c1,-9.514708773011364,0.0404704232905398,-10.5047 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+## System Details +- Ligands: 20 +- Host Atoms: 4820 +- Map Details: + - Edges: 34 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 29 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 6.54 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 2494.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1ccc_amber14.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/gpcrs/p2y1_meta_sub/ddg_results.csv b/summaries/2026_june_08/gpcrs/p2y1_meta_sub/ddg_results.csv new file mode 100644 index 0000000..e50d194 --- /dev/null +++ b/summaries/2026_june_08/gpcrs/p2y1_meta_sub/ddg_results.csv @@ -0,0 +1,29 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +11a,1,-1.9074582912634934,0.04823249338196401,0.7822962772514267,0.04892566371101626,-1.9453700000000005,-2.6897545685149202,0.06870294016564833,-2.689754565820733,0.11015767662888043 +11a,6b,3.5498246137602436,0.05635301540452302,4.603435884876913,0.0572935507644353,-2.2222700000000017,-1.0536112711166696,0.08036300955277455,-0.27730425607369824,0.08140761584682994 +11a,6f,5.272487935686196,0.0604948200793683,5.814073594549572,0.05874618418765592,-1.554780000000001,-0.5415856588633754,0.08432518848508516,-1.3963290868838794,0.07496286681040967 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b/summaries/2026_june_08/gpcrs/p2y1_meta_sub/dg_results.csv new file mode 100644 index 0000000..8e13dbb --- /dev/null +++ b/summaries/2026_june_08/gpcrs/p2y1_meta_sub/dg_results.csv @@ -0,0 +1,20 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11a,O=C(Nc1ccc(F)cc1F)Nc1cccnc1Oc1ccccc1,-7.728713535195606,0.064048635315432,-7.774799999999999 +1,O=C(Nc1ccc(F)cc1F)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-10.41846810101634,0.08962413756630401,-9.72017 +6b,O=C(Nc1ccccc1F)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-8.006017791269304,0.050249101803871404,-9.99707 +6f,O=C(Nc1ccc(F)cc1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-9.125042622079485,0.03895129926800923,-9.32958 +11c,CC(C)(C)c1cccc(Oc2ncccc2NC(=O)Nc2ccc(F)cc2F)c1,-10.64961828762516,0.06791914860815908,-10.2066 +6a,O=C(Nc1ccccc1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-7.92641393158694,0.06020691491996897,-9.23186 +6e,O=C(Nc1cccc(Cl)c1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-9.295458622984688,0.06013111283357136,-9.40347 +6q,O=C(Nc1cc(Cl)cc(Cl)c1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-10.198478535155484,0.06590392681307966,-9.23883 +6d,O=C(Nc1cccc(F)c1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-7.996294199236714,0.0693403394013686,-8.48127 +6p,O=C(Nc1ccc(Cl)c(Cl)c1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-10.935214695261669,0.052851811332670126,-9.65303 +16,CC(C)(C)c1ccccc1Oc1ncccc1NC(=O)Nc1ccc(OC(F)(F)F)cc1,-15.32728350002677,0.07948298899587743,-11.2166 +6h,Cc1ccc(NC(=O)Nc2cccnc2Oc2cccc(C(F)(F)F)c2)cc1,-8.941700988109709,0.0424225636006731,-9.98459 +6n,N#Cc1ccc(NC(=O)Nc2cccnc2Oc2cccc(C(F)(F)F)c2)cc1,-8.632402337612238,0.04840570608797913,-8.51749 +6g,O=C(Nc1ccc(Cl)cc1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-9.546223744996343,0.05229456663819348,-9.76958 +6j,O=C(Nc1ccc(OC(F)(F)F)cc1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-10.699135415333503,0.07544684411371547,-8.87368 +6l,COc1ccc(NC(=O)Nc2cccnc2Oc2cccc(C(F)(F)F)c2)cc1,-8.005319519460075,0.07386965643225497,-10.4744 +6i,CC(C)(C)c1ccc(NC(=O)Nc2cccnc2Oc2cccc(C(F)(F)F)c2)cc1,-10.235397988290684,0.14590349546759196,-10.2436 +6m,CN(C)c1ccc(NC(=O)Nc2cccnc2Oc2cccc(C(F)(F)F)c2)cc1,-6.5154030591885235,0.12116248726516206,-8.58909 +6k,O=C(Nc1ccc(-c2ccccc2)cc1)Nc1cccnc1Oc1cccc(C(F)(F)F)c1,-10.827023125570783,0.10218735536556714,-10.3039 diff --git a/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/README.md b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/README.md new file mode 100644 index 0000000..88c0d13 --- /dev/null +++ b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/README.md @@ -0,0 +1,40 @@ +# P2Y1 Ortho Sub Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.19 +- RMSE: 1.46 +- R²: 0.92 +- Kendall 𝜏: 0.75 +- Spearman ρ: 0.88 + +## System Details +- Ligands: 12 +- Host Atoms: 4820 +- Map Details: + - Edges: 21 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 14 + - Mean Dummy Atoms: 6.9 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 5.12 Hours +- Average Time Per Edge: 0.24 Hours +- Total Nanoseconds Simulated: 1986.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1ccc_amber14.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/ddg_results.csv b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/ddg_results.csv new file mode 100644 index 0000000..04c6bde --- /dev/null +++ b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/ddg_results.csv @@ -0,0 +1,22 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +11b,11d,-7.613261189454912,0.04547515301080555,-8.751959700873353,0.049084765781064535,0.26179999999999914,1.138698511418443,0.0669126577946067,1.322295811569953,0.045045367946886 +11b,12,5.684799851834576,0.04773241660717993,6.5111778822336355,0.04507956648914519,-0.5595999999999997,-0.8263780303990591,0.06565478588808776,-0.7244615476577927,0.06576825687227345 +11b,13,8.4600985630643,0.06188819081378338,9.94219566342839,0.061414816330035565,0.06240000000000023,-1.48209710036409,0.08718903501619492,-0.3697908681106412,0.06367124666388975 +11b,14,-5.331917333442974,0.053121134964466556,-9.826944133029283,0.051967636856884505,1.3475400000000004,4.4950267995863085,0.07431345948347508,3.5564107557456417,0.06500256764162836 +11b,17,,,15.28266372921589,0.05975412686746356,-0.48050000000000104,,,-1.4370525519609494,0.07448915371918235 +11d,11a,-2.776356189456363,0.05210401079907852,-8.411993044029611,0.055496866518701324,2.5291000000000015,5.635636854573248,0.07612312483565715,5.579294009005291,0.06810925343077996 +11d,11f,6.867632640334855,0.05340750646234684,5.762461304114308,0.05450812497485315,1.0754900000000003,1.1051713362205475,0.07631184334557663,1.089430707781725,0.060689640478069976 +11d,18,14.076728840098625,0.05609209465829137,14.790444724291573,0.05580997589646051,-0.8213999999999988,-0.7137158841929493,0.07912696438457767,-0.8742685853674406,0.06086187211453519 +11d,19,12.491528877590964,0.052463186338047856,14.48169881389089,0.0529903258449307,-0.3315999999999999,-1.9901699362999266,0.07456782519218769,-1.6195763238257452,0.05670401669614086 +11e,11a,-0.39585586525686545,0.04910219055791277,-4.265417218375016,0.051588822510210755,1.929780000000001,3.8695613531181516,0.07122100621007545,4.252201708540086,0.08238630987952386 +11e,11d,3.1163378594056446,0.043220023308722495,4.394959188900644,0.04508633912265143,-0.5993200000000005,-1.278621329494999,0.062455971614324,-1.327092300465205,0.06348372046405526 +11e,11f,10.21828160710951,0.05232099019369716,10.107573268603833,0.05283357157808549,0.47616999999999976,0.11070833850567817,0.07435638708642073,-0.2376615926834802,0.07636665577347294 +11f,11a,-8.980372537177898,0.050468788026051176,-13.81486867521291,0.05193729804146572,1.4536100000000012,4.834496138035012,0.07241948282517988,4.489863301223566,0.08025306070776375 +12,13,3.1223105193683196,0.0552055852845079,2.75497261549387,0.05451047025729073,0.6219999999999999,0.36733790387444964,0.07758252389730598,0.3546706795471515,0.078758301328191 +14,12,12.299311136668265,0.03628776529188043,16.499890586086842,0.04244534575115013,-1.90714,-4.200579449418577,0.055842719183554095,-4.280872303403434,0.07983843796300572 +14,13,16.462650263816894,0.05469533929307598,19.51562807892988,0.05534850412308748,-1.2851400000000002,-3.0529778151129836,0.07781411857142721,-3.926201623856283,0.07812003722534483 +16,11b,-12.563671166360429,0.05494629030607006,-14.266252639084158,0.05654284321195755,0.6509,1.70258147272373,0.07884280523225276,1.9574838298380506,0.05923840348539533 +16,17,8.510463087089603,0.05612777642999983,7.845320403720562,0.054704228181697574,0.170399999999999,0.6651426833690409,0.078376526255833,0.5204312778771012,0.08295300617608366 +16,19,-7.38282989208279,0.04779563063025433,-9.127312301389384,0.05045496125866512,0.5810999999999993,1.7444824093065954,0.06949910375650252,1.6602033175822584,0.06852334480674724 +17,18,-7.231748122603482,0.04455789682507364,-9.220483835713965,0.04913962502087141,-0.07909999999999862,1.9887357131104828,0.0663333167922859,1.8850797781634618,0.08499244863878007 +18,19,-8.387183184085847,0.05526766013607474,-7.936531554870641,0.05416974770947759,0.4897999999999989,-0.4506516292152064,0.07738782736209306,-0.7453077384583047,0.07097861562097889 diff --git a/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/dg_plot.png b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/dg_plot.png new file mode 100644 index 0000000..3dd33c8 Binary files /dev/null and b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/dg_plot.png differ diff --git a/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/dg_results.csv b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/dg_results.csv new file mode 100644 index 0000000..6f68572 --- /dev/null +++ b/summaries/2026_june_08/gpcrs/p2y1_ortho_sub/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11b,CC(C)(C)c1ccccc1Oc1ncccc1NC(=O)Nc1ccc(F)cc1F,-11.245926577971414,0.032989553161941285,-10.5657 +11d,CC(C)c1ccccc1Oc1ncccc1NC(=O)Nc1ccc(F)cc1F,-9.92363076640146,0.030672048442283648,-10.3039 +12,Cc1ccc(NC(=O)Nc2cccnc2Oc2ccccc2C(C)(C)C)cc1,-11.970388125629206,0.05689598399002158,-11.1253 +13,Cc1ccc(NC(=O)Nc2cccnc2Sc2ccccc2C(C)(C)C)cc1,-11.615717446082055,0.05445839727635529,-10.5033 +14,Cc1ccc(NC(=O)Nc2cccnc2Nc2ccccc2C(C)(C)C)cc1,-7.689515822225772,0.05600913481013539,-9.21816 +17,CC(C)(C)c1ccc(NC(=O)Nc2cccnc2Oc2ccccc2C(C)(C)C)cc1,-12.682979129932363,0.06678565268061268,-11.0462 +11a,O=C(Nc1ccc(F)cc1F)Nc1cccnc1Oc1ccccc1,-4.34433675739617,0.06081197124951976,-7.774799999999999 +11f,O=C(Nc1ccc(F)cc1F)Nc1cccnc1Oc1ccccc1C(F)(F)F,-8.834200058619736,0.05236848198784833,-9.22841 +18,CC(C)c1ccccc1Oc1ncccc1NC(=O)Nc1ccc(C(C)(C)C)cc1,-10.797899351768901,0.05256798380801989,-11.1253 +19,CC(C)c1ccccc1Oc1ncccc1NC(=O)Nc1ccc(OC(F)(F)F)cc1,-11.543207090227206,0.04769246223283536,-10.6355 +11e,CCc1ccccc1Oc1ncccc1NC(=O)Nc1ccc(F)cc1F,-8.596538465936256,0.05558244514514015,-9.70458 +16,CC(C)(C)c1ccccc1Oc1ncccc1NC(=O)Nc1ccc(OC(F)(F)F)cc1,-13.203410407809464,0.049202416908866856,-11.2166 diff --git a/summaries/2026_june_08/jacs_set/bace/README.md b/summaries/2026_june_08/jacs_set/bace/README.md new file mode 100644 index 0000000..9357b67 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/bace/README.md @@ -0,0 +1,40 @@ +# Bace Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.21 +- RMSE: 1.51 +- R²: 0.20 +- Kendall 𝜏: 0.31 +- Spearman ρ: 0.44 + +## System Details +- Ligands: 36 +- Host Atoms: 6101 +- Map Details: + - Edges: 61 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 5.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.05 Hours +- Average Time Per Edge: 0.10 Hours +- Total Nanoseconds Simulated: 6034.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/bace/ddg_results.csv b/summaries/2026_june_08/jacs_set/bace/ddg_results.csv new file mode 100644 index 0000000..26a19f5 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/bace/ddg_results.csv @@ -0,0 +1,62 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CAT-13a,CAT-13o,-7.905318650844416,0.04710145204363286,-8.405386270850794,0.047304587955753465,0.3000000000000007,0.5000676200063775,0.06675530560399123,1.0455304740434928,0.06867268438231774 +CAT-13a,CAT-13i,23.133298416707614,0.05135765722247212,24.531228958783597,0.05122991556504185,-0.4299999999999997,-1.3979305420759836,0.0725404246209123,-1.4094047991381782,0.06834380724648483 +CAT-13b,CAT-13h,16.59541495567661,0.049243496127373956,21.155590948106642,0.04692593997961346,-0.5099999999999998,-4.5601759924300325,0.06802180351782051,-4.046862429529483,0.07912162246752144 +CAT-13b,CAT-13i,17.920352401965882,0.049570984315019606,20.142443648736492,0.04915446386724256,-0.15000000000000036,-2.2220912467706078,0.06981005517857705,-2.5751268768480173,0.07143501685157864 +CAT-13b,CAT-13k,5.585016743913421,0.06456070315175427,5.575876169671592,0.06580108894138224,-0.5800000000000001,0.009140574241828937,0.09218387981269084,-0.31801777131621023,0.07216618508551695 +CAT-13c,CAT-13f,23.962802859321616,0.06274577316156138,25.69356882035209,0.06131451239247038,0.23000000000000043,-1.7307659610304718,0.0877297069388045,-2.154944773391027,0.09640405498564017 +CAT-13d,CAT-13a,-14.825754482617093,0.04647779933956343,-16.830026801088493,0.04420527991941369,1.6300000000000008,2.004272318471401,0.06414275176668399,2.4989044741086417,0.06484762196570544 +CAT-13d,CAT-13c,-25.551665361448205,0.05960628795544261,-28.149874565913194,0.0600017224402919,1.1500000000000004,2.5982092044649896,0.08457609744856387,2.2166751790704717,0.0783342595214496 +CAT-13d,CAT-13i,-20.359556675429452,0.05911727017520618,-20.944258186230204,0.05718351642524752,1.200000000000001,0.5847015108007517,0.08224844183159262,1.0894996749704635,0.06679410676974509 +CAT-13d,CAT-17d,-6.478270201204095,0.04588579980904929,-9.175648616370276,0.046919818758905295,1.0500000000000007,2.697378415166181,0.06562755531394317,2.749477318834595,0.07015448317212782 +CAT-13d,CAT-17i,-7.396685594491503,0.041836335335213165,-7.620079758913304,0.04202244512271969,1.0,0.22339416442180152,0.059297258354601805,-0.03411039312974218,0.07136937589486834 +CAT-13e,CAT-13c,-57.21582167303197,0.06611364528445247,-59.67809004970027,0.06679483825681869,0.6399999999999988,2.462268376668304,0.09398172434336888,2.446590207239555,0.08942825273971923 +CAT-13e,CAT-13d,-28.31662319009113,0.060742938657868506,-28.31779131279411,0.06159465688518505,-0.5100000000000016,0.0011681227029805355,0.08650783983892588,0.22991502816908316,0.07653069291556011 +CAT-13e,CAT-13f,-33.4732683289128,0.06920164589483614,-34.04079432364071,0.06923289549515142,0.8699999999999992,0.5675259947279102,0.09788800546132734,0.2916454338485277,0.09494436560974157 +CAT-13g,CAT-13m,-74.93870599540531,0.07203607577893342,-75.56811874018634,0.07113143269002255,0.33000000000000007,0.6294127447810317,0.1012367370580633,1.0388825815365692,0.10584128699206576 +CAT-13g,CAT-4p,-33.77509586780955,0.07456598661961657,-32.993709433103305,0.07206284119437896,-0.9900000000000002,-0.7813864347062411,0.10369734539303847,-0.5657582255090539,0.10672229362741092 +CAT-13h,CAT-17a,-10.037119698692015,0.04955122458013149,-9.248672957299815,0.0509057641777531,-1.1000000000000014,-0.7884467413921987,0.07104027508330495,-0.6532819275237411,0.0857105575202735 +CAT-13h,CAT-17i,-15.97285912273343,0.050380378475882295,-15.881279182622077,0.051832894770206105,0.15999999999999837,-0.09157994011135419,0.07228299603386956,0.34812548458126,0.08195437291120171 +CAT-13j,CAT-13g,37.143591790509994,0.07295983997131203,43.179829436999505,0.0729449034052485,-0.35999999999999943,-6.036237646489515,0.10317023398946275,-5.397536052934665,0.10635689577175489 +CAT-13j,CAT-13o,-9.127042603942703,0.05722115706093382,-10.246185371753963,0.05861572021898627,0.19000000000000128,1.1191427678112604,0.08191497709321863,-0.5507026297558104,0.08497688682502436 +CAT-13j,CAT-4i,-0.16899746065765026,0.055168944466972666,3.6289383451853507,0.05412885058601274,0.47000000000000064,-3.797935805843001,0.07728871133201022,-3.386378280224962,0.09954359042167381 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a/summaries/2026_june_08/jacs_set/bace/dg_comparison_plot.png b/summaries/2026_june_08/jacs_set/bace/dg_comparison_plot.png new file mode 100644 index 0000000..09865fc Binary files /dev/null and b/summaries/2026_june_08/jacs_set/bace/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/bace/dg_plot.png b/summaries/2026_june_08/jacs_set/bace/dg_plot.png new file mode 100644 index 0000000..d4ffef7 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/bace/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/bace/dg_results.csv b/summaries/2026_june_08/jacs_set/bace/dg_results.csv new file mode 100644 index 0000000..c2762b8 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/bace/dg_results.csv @@ -0,0 +1,37 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CAT-13a,CN1C(=O)[C@@](C)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-7.430588168235953,0.04698211023561845,-8.843 +CAT-13o,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(c2nccs2)[NH+]=C1N,-6.385057694192461,0.05008611482318852,-8.543 +CAT-13i,CN1C(=O)[C@@](CC2CC2)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-8.839992967374132,0.04963423522885055,-9.273 +CAT-13b,CC[C@]1(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C(N)N(C)C1=O,-6.264866090526114,0.05137513334126206,-9.123 +CAT-13h,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2(C)CC2)[NH+]=C1N,-10.311728520055597,0.0601733065076246,-9.633 +CAT-13k,CN1C(=O)[C@@](c2cccnc2)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-6.582883861842324,0.050680903148667675,-9.703 +CAT-13c,CC(C)[C@]1(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C(N)N(C)C1=O,-7.712817463274123,0.06433009266555255,-9.323 +CAT-13f,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CCCC2)[NH+]=C1N,-9.86776223666515,0.07180098185481697,-9.093 +CAT-13d,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CC2)[NH+]=C1N,-9.929492642344595,0.04469782312837214,-10.473 +CAT-17d,CN1C(=O)[C@](c2cccc(-c3cccnc3)c2)(C2CC2)[NH+]=C1N,-7.18001532351,0.05407176820424062,-9.423 +CAT-17i,Cc1cncc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-9.963603035474337,0.05563894699945152,-9.473 +CAT-13e,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CCC2)[NH+]=C1N,-10.159407670513678,0.062121265004187756,-9.963 +CAT-13g,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CCCCC2)[NH+]=C1N,-11.231891117371315,0.08123630273352278,-9.093 +CAT-13m,CN1C(=O)[C@@](c2cncnc2)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-10.193008535834746,0.06784571578459665,-8.763 +CAT-4p,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cncc(Cl)c3)c2)[NH+]=C1N,-11.79764934288037,0.06921207319017943,-10.083 +CAT-17a,CN1C(=O)[C@](c2cccc(-c3cc(Cl)cc(Cl)c3)c2)(C2CC2)[NH+]=C1N,-10.965010447579338,0.061036651729723626,-10.733 +CAT-13j,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(c2ccccn2)[NH+]=C1N,-5.83435506443665,0.06864730436361921,-8.733 +CAT-4i,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3ccccn3)c2)[NH+]=C1N,-9.220733344661612,0.07208657293592598,-8.263 +CAT-4n,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cncc(C#N)c3)c2)[NH+]=C1N,-11.551646575787565,0.06194393241538891,-9.093 +CAT-4b,COc1cccc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)c1,-11.945742613879005,0.06680116924339197,-9.633 +CAT-4d,CCOc1cccc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)c1,-11.453617076244221,0.06671719499779474,-9.113 +CAT-13n,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(c2ncccn2)[NH+]=C1N,-8.091490828927927,0.06502036618568624,-8.543 +CAT-17h,CN1C(=O)[C@](c2cccc(-c3cncc(Cl)c3)c2)(C2CC2)[NH+]=C1N,-10.374343314072798,0.05570880339299171,-10.333 +CAT-17b,COc1cccc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-9.702307298604365,0.06892240061474357,-10.023 +CAT-17c,CN1C(=O)[C@](c2cccc(-c3cccc(C#N)c3)c2)(C2CC2)[NH+]=C1N,-9.490299690966904,0.07865769551519228,-9.863 +CAT-17e,COc1cncc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-9.911659830661572,0.07967938633734753,-10.023 +CAT-17f,CN1C(=O)[C@](c2cccc(-c3cncc(C#N)c3)c2)(C2CC2)[NH+]=C1N,-9.848606489867777,0.06603961143674238,-9.423 +CAT-24,CC#Cc1cncc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-12.633270023191582,0.06779731515188107,-11.35 +CAT-17g,CN1C(=O)[C@](c2cccc(-c3cncc(F)c3)c2)(C2CC2)[NH+]=C1N,-8.459643360668036,0.05914072006840316,-9.743 +CAT-4a,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3ccccc3)c2)[NH+]=C1N,-8.94129192779183,0.06777758699739767,-7.933000000000001 +CAT-4c,COc1ccc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)cc1,-9.44101772401997,0.069958742671095,-7.853 +CAT-4k,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3ccncc3)c2)[NH+]=C1N,-7.930028132381838,0.0730532820686038,-7.853 +CAT-4l,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cnccn3)c2)[NH+]=C1N,-7.707839977085033,0.06898365510562263,-9.343 +CAT-4o,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cncc(F)c3)c2)[NH+]=C1N,-9.452885838558494,0.0670257432807211,-9.383 +CAT-4j,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cccnc3)c2)[NH+]=C1N,-8.76847494857835,0.06989150219387438,-9.023 +CAT-4m,Cc1cncc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)c1,-10.639970821940205,0.0683205880361884,-9.153 diff --git a/summaries/2026_june_08/jacs_set/cdk2/README.md b/summaries/2026_june_08/jacs_set/cdk2/README.md new file mode 100644 index 0000000..9abb65d --- /dev/null +++ b/summaries/2026_june_08/jacs_set/cdk2/README.md @@ -0,0 +1,40 @@ +# Cdk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.66 +- RMSE: 0.76 +- R²: 0.67 +- Kendall 𝜏: 0.58 +- Spearman ρ: 0.79 + +## System Details +- Ligands: 16 +- Host Atoms: 9028 +- Map Details: + - Edges: 28 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 5.9 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 4.88 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 2911.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/cdk2/ddg_results.csv b/summaries/2026_june_08/jacs_set/cdk2/ddg_results.csv new file mode 100644 index 0000000..3fdbaa3 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/cdk2/ddg_results.csv @@ -0,0 +1,29 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +17,1h1q,0.19625884550600664,0.046524381964603255,-0.7364998284629116,0.045057734630122255,-1.1399999999999997,0.9327586739689183,0.0647666393074924,0.890811250917567,0.06113661166152829 +17,1oi9,-13.852134324857108,0.05388541601485503,-12.283136607285186,0.05361503771566021,-2.7,-1.5689977175719216,0.07601454024294077,-1.3920993543736504,0.05951897457019645 +17,1oiu,-87.05018271021022,0.04310811697730781,-84.57682858899898,0.044559026144981945,-2.04,-2.4733541212112424,0.06199852063007987,-2.552593144532926,0.06826118357951876 +1h1r,1h1q,1.5323113634571999,0.045762544236106886,-0.23029463014029067,0.04372176707712518,-0.5100000000000007,1.7626059935974905,0.06329141625298036,1.6687267798146728,0.06548573403263154 +1h1r,1oi9,-11.968621671018118,0.05292978350774748,-11.60665696100796,0.052443305058062065,-2.070000000000001,-0.3619647100101571,0.07451081953374272,-0.6141838254765446,0.06397815572699585 +1h1r,1oiu,-85.93459175789451,0.045199837086527375,-83.88021824281684,0.04492726035238052,-1.410000000000001,-2.0543735150776716,0.0637297732258573,-1.7746776156358202,0.07218230572665853 +1h1s,29,58.63155103174715,0.06029417707620481,56.29417285871173,0.06074991094055374,1.3699999999999992,2.3373781730354235,0.08559170210120812,1.9981835645150134,0.07705394722764894 +1h1s,31,61.104939725338774,0.055216909175278994,58.15746151321671,0.05429415334733172,1.7100000000000009,2.947478212122063,0.07743876384973214,3.1373901473112316,0.07498843955478793 +1h1s,32,16.599366708505475,0.05514364267490255,15.451876711950817,0.05230290648161514,1.5,1.1474899965546579,0.07600273254220477,1.0586385313071158,0.07291562338870025 +1oiu,1h1q,86.79072084422701,0.05870114810160084,83.67678065618072,0.058157887573163904,0.9000000000000004,3.1139401880462843,0.08263270947644673,3.443404395450493,0.06348041241043122 +1oiy,1oi9,10.215564222772503,0.04807647735404249,10.571630937519384,0.04671625137182499,0.049999999999998934,-0.3560667147468801,0.0670354817765137,-0.37085736737146213,0.05272345946411556 +1oiy,26,17.075610232499535,0.051447289622329695,16.612241014996183,0.05090277721961524,1.3599999999999994,0.4633692175033497,0.0723734505060637,0.6344423871172875,0.0583608243835718 +1oiy,29,6.532828269107519,0.067397892363179,7.820280640780814,0.06614864255122492,-0.09000000000000163,-1.287452371673295,0.09443579197723916,-0.6111285302030769,0.06920143010581399 +1oiy,31,5.848772601839102,0.06754492232983068,5.145972031284023,0.06774557385260202,0.25,0.7028005705550797,0.09566493249441622,0.5280780525931412,0.06689389517878769 +20,1h1q,8.65296055667878,0.049566668880134564,6.107302890018488,0.05000786154809497,0.5400000000000009,2.545657666660293,0.07041051683155249,1.9511068211184739,0.063711741786904 +21,1h1q,-1.4120600048944394,0.053067416754551476,-2.4264767734738886,0.05013856486724268,-0.35000000000000053,1.014416768579449,0.07300702985293918,1.4970879871148153,0.06775316612052584 +21,20,-7.904412124104333,0.052287482220350075,-7.994154504130341,0.04952050772893723,-0.8900000000000015,0.08974238002600869,0.07201570302840317,-0.4540188340036586,0.07444339258324081 +22,20,-8.646798846593503,0.048167199487982856,-6.942296015775728,0.04539869876006956,-0.8600000000000003,-1.704502830817774,0.06619003667941784,-1.7705687835195976,0.06722745294088837 +22,21,0.5314853261273519,0.051144783189113044,1.771742171589048,0.052185492155705324,0.030000000000001137,-1.2402568454616962,0.07306924413865633,-1.316549949515939,0.0710692331937935 +22,32,-66.97314606497847,0.06742776203590346,-63.42606906623568,0.06687871043749438,-1.8899999999999997,-3.5470769987427904,0.09496981100830225,-3.2821887637318534,0.06900346657259096 +26,1h1q,1.9638528230833188,0.05100644856061972,0.7608793445954164,0.0502649061375727,0.25,1.2029734784879025,0.07161158135236324,1.2776108508024677,0.05948869266402845 +26,1oi9,-11.910860488341994,0.042663304911530094,-10.84178130751507,0.04125946803696216,-1.3100000000000005,-1.0690791808269222,0.0593506637592815,-1.0052997544887496,0.05782497387211175 +28,1h1s,-28.82312590673097,0.0517706827575135,-29.055214976584143,0.054417845376918364,-0.14000000000000057,0.2320890698531737,0.0751099559888388,0.06276955593565248,0.07663002364426101 +28,1oiy,21.02862681626088,0.06799890635291889,19.147337087839922,0.06752162761701304,1.3200000000000003,1.8812897284209558,0.0958280828423673,2.672081650653743,0.0687290889583774 +28,30,24.696892824885236,0.052203435609444085,22.556059324319715,0.05208818393232961,1.299999999999999,2.1408335005655226,0.07374535642871066,1.8357329648496012,0.08085488889005513 +30,29,9.395348595494308,0.06232012838548907,8.937304324940182,0.06323587309876837,-0.07000000000000028,0.45804427055412616,0.08878386141944591,0.22522015560106468,0.08125677397647821 +30,31,7.940260842712921,0.04475734468766711,6.523772382648888,0.04621770038517752,0.27000000000000135,1.4164884600640337,0.06433735876133463,1.3644267383972828,0.07930081084431131 +30,32,-37.723084864769234,0.06084215865540054,-37.11191388256458,0.060605339311762214,0.0600000000000005,-0.611170982204658,0.08587651263845522,-0.7143248776068329,0.0773436530548301 diff --git a/summaries/2026_june_08/jacs_set/cdk2/dg_comparison_plot.png b/summaries/2026_june_08/jacs_set/cdk2/dg_comparison_plot.png new file mode 100644 index 0000000..a7868c0 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/cdk2/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/cdk2/dg_plot.png b/summaries/2026_june_08/jacs_set/cdk2/dg_plot.png new file mode 100644 index 0000000..277b715 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/cdk2/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/cdk2/dg_results.csv b/summaries/2026_june_08/jacs_set/cdk2/dg_results.csv new file mode 100644 index 0000000..037337b --- /dev/null +++ b/summaries/2026_june_08/jacs_set/cdk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,Brc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.850309009308583,0.046730673595246026,-7.04 +1h1q,c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-6.9594977583910165,0.03941991160298426,-8.18 +1oi9,Oc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.242408363682234,0.03686125987025223,-9.74 +1oiu,NS(=O)(=O)c1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-10.40290215384151,0.049757746422153575,-9.08 +1h1r,Clc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.62822453820569,0.052291987254315206,-7.669999999999999 +1h1s,NS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.480863091028862,0.050690073518524476,-11.25 +29,CN(C)S(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.482679526513849,0.058032983983661315,-9.88 +31,C[S@](=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.34347294371763,0.05526103974364459,-9.54 +32,COc1cc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)ccc1S(N)(=O)=O,-10.422224559721746,0.052413782355878055,-9.75 +1oiy,NC(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.871550996310772,0.037696295555955744,-9.79 +26,COc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.237108609193484,0.04455305964900884,-8.43 +20,OCc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.91060457950949,0.05005253850439593,-8.72 +21,COc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.456585745505832,0.05510500965038004,-7.829999999999999 +22,CSc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.140035795989893,0.044880661962423456,-7.86 +28,CNS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.543632646964515,0.057468921778702144,-11.11 +30,CS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.707899682114913,0.056875619442926295,-9.81 diff --git a/summaries/2026_june_08/jacs_set/jnk1/README.md b/summaries/2026_june_08/jacs_set/jnk1/README.md new file mode 100644 index 0000000..28e2e34 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/jnk1/README.md @@ -0,0 +1,40 @@ +# Jnk1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.29 +- RMSE: 1.47 +- R²: 0.51 +- Kendall 𝜏: 0.57 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 21 +- Host Atoms: 5993 +- Map Details: + - Edges: 36 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 13 + - Mean Dummy Atoms: 6.5 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.40 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 3645.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/jnk1/ddg_results.csv b/summaries/2026_june_08/jacs_set/jnk1/ddg_results.csv new file mode 100644 index 0000000..f5ab6f8 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/jnk1/ddg_results.csv @@ -0,0 +1,37 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +17124-1,18631-1,-4.983747869075262,0.05677687737915152,-7.43202088881482,0.05626018526231395,0.2699999999999996,2.4482730197395575,0.07993010853662777,2.2197660900685996,0.0628079763005726 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a/summaries/2026_june_08/jacs_set/jnk1/dg_comparison_plot.png b/summaries/2026_june_08/jacs_set/jnk1/dg_comparison_plot.png new file mode 100644 index 0000000..c482011 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/jnk1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/jnk1/dg_plot.png b/summaries/2026_june_08/jacs_set/jnk1/dg_plot.png new file mode 100644 index 0000000..9ba5b12 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/jnk1/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/jnk1/dg_results.csv b/summaries/2026_june_08/jacs_set/jnk1/dg_results.csv new file mode 100644 index 0000000..6917ccd --- /dev/null +++ b/summaries/2026_june_08/jacs_set/jnk1/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17124-1,CCOc1nc(NC(=O)Cc2cc(OC)c(Br)cc2OC)cc(N)c1C#N,-10.903264244217262,0.05121551239344867,-9.68 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a/summaries/2026_june_08/jacs_set/mcl1/README.md b/summaries/2026_june_08/jacs_set/mcl1/README.md new file mode 100644 index 0000000..edb9fcf --- /dev/null +++ b/summaries/2026_june_08/jacs_set/mcl1/README.md @@ -0,0 +1,40 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.45 +- RMSE: 1.90 +- R²: 0.44 +- Kendall 𝜏: 0.48 +- Spearman ρ: 0.66 + +## System Details +- Ligands: 42 +- Host Atoms: 2542 +- Map Details: + - Edges: 74 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.83 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 8112.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/mcl1/ddg_results.csv b/summaries/2026_june_08/jacs_set/mcl1/ddg_results.csv new file mode 100644 index 0000000..58caabc --- /dev/null +++ b/summaries/2026_june_08/jacs_set/mcl1/ddg_results.csv @@ -0,0 +1,75 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +23,44,-0.6891572568656321,0.06265844711925944,-0.8545116638616783,0.0641309920063712,0.16000000000000014,0.16535440699604612,0.0896597185536419,0.08795724841545827,0.07867992569726544 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b/summaries/2026_june_08/jacs_set/mcl1/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/mcl1/dg_results.csv b/summaries/2026_june_08/jacs_set/mcl1/dg_results.csv new file mode 100644 index 0000000..970ca66 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/mcl1/dg_results.csv @@ -0,0 +1,43 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +23,O=C([O-])c1sc2ccccc2c1CCCOc1cccc2ccccc12,-8.237242562213627,0.05153622064189414,-8.83 +44,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-8.149285313798169,0.059452070356525125,-8.67 +51,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-6.24037319101107,0.06556265469725027,-8.45 +54,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-9.1841202216379,0.06226346922647166,-9.78 +57,Cn1c(C(=O)[O-])c(CCCOc2cccc3ccccc23)c2ccccc21,-8.122701032107036,0.06298404173401645,-9.04 +62,O=C([O-])c1sc2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-6.0208955633854995,0.06392793422001183,-7.959999999999999 +64,O=C([O-])c1sc2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-9.988770255601048,0.06634909496221666,-9.5 +66,O=C([O-])c1sc2c(Cl)cccc2c1CCCOc1cccc2ccccc12,-9.700285991533534,0.06589891444392657,-8.43 +26,O=C([O-])c1oc2ccccc2c1CCCOc1cccc2ccccc12,-8.640969985828763,0.06327540544228699,-8.24 +68,O=C([O-])c1oc2ccc(Cl)cc2c1CCCOc1cccc2ccccc12,-7.825528450073685,0.061542811435291445,-7.690000000000001 +27,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1,-5.057779513233338,0.04513531198865886,-6.12 +29,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1C(F)(F)F,-2.793728741939713,0.054396134989785926,-6.94 +31,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(C(F)(F)F)c1,-8.208936270965369,0.059453647413879956,-7.920000000000001 +32,Cc1ccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc1,-6.3828128366981485,0.05929089369535692,-6.58 +38 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(-c2ccccc2)c1,-11.474081646518115,0.06542546350343953,-7.02 +39,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(-c2ccccc2)cc1,-6.340338443935522,0.07238113727095624,-7.03 +40 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(Oc2ccccc2)c1,-6.8232987725525485,0.06691384901483133,-7.25 +41 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Oc2ccccc2)cc1,-9.289626032220736,0.06427050344272672,-7.13 +48 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2[nH]ccc12,-1.3448647970534422,0.06626630106999538,-6.66 +28,Cc1ccccc1OCCCc1c(C(=O)[O-])[nH]c2ccccc12,-4.385173179798426,0.06153450072232984,-6.62 +42,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2ccccc12,-7.258328623946449,0.04829164817636556,-8.9 +45,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2c1CCCC2,-8.864492250003893,0.06029562246261847,-8.95 +30 flip,Cc1cccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)c1,-5.155379843791793,0.05502392683295173,-7.85 +37,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc(C)c1Cl,-9.098514088736259,0.0602395298310321,-8.95 +46 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2c(c1)CCC2,-6.7224344410299866,0.07224403515407563,-7.6 +47 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ncccc2c1,-4.412348574919006,0.0650356380118988,-5.78 +34,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(C(F)(F)F)cc1,-8.000729843318982,0.06338012352330478,-6.87 +33,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)cc1,-6.694628995541039,0.06583824910550048,-6.88 +43 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ccccc2c1,-6.178678912003848,0.07054468637082875,-7.03 +35,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-8.459751388344003,0.04699695313836142,-8.81 +36,CCc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-10.305101558552218,0.05887559684327623,-8.18 +49,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)ccc1Cl,-7.871659090620597,0.059073819006055614,-8.36 +52,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)ccc1Cl,-10.505008997125712,0.06353057662448001,-9.23 +50,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)cc(C)c1Cl,-8.23057258571828,0.06795016389971376,-9.33 +65,Cc1cc(OCCCc2c(C(=O)[O-])sc3c(Cl)cccc23)cc(C)c1Cl,-11.507489556405403,0.06322922281308851,-8.41 +61,Cc1cc(OCCCc2c(C(=O)[O-])sc3cccc(Cl)c23)cc(C)c1Cl,-9.001442820089256,0.06861861357299014,-8.08 +53,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)cc(C)c1Cl,-11.645720676798295,0.06807134926198256,-9.96 +58,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3cc(Cl)ccc23)cc(C)c1Cl,-12.26577241735001,0.07418344070212152,-9.41 +63,Cc1cc(OCCCc2c(C(=O)[O-])sc3cc(Cl)ccc23)cc(C)c1Cl,-11.96347004464009,0.06909362807523234,-9.06 +56,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3ccccc23)cc(C)c1Cl,-10.366882263297722,0.0778625015966893,-9.26 +60,Cc1cc(OCCCc2c(C(=O)[O-])sc3ccccc23)cc(C)c1Cl,-10.163297677000687,0.06401702541844158,-8.92 +67,Cc1cc(OCCCc2c(C(=O)[O-])oc3ccccc23)cc(C)c1Cl,-10.377482548660785,0.08307737445093281,-7.58 diff --git a/summaries/2026_june_08/jacs_set/p38/README.md b/summaries/2026_june_08/jacs_set/p38/README.md new file mode 100644 index 0000000..e49d60f --- /dev/null +++ b/summaries/2026_june_08/jacs_set/p38/README.md @@ -0,0 +1,40 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.05 +- RMSE: 1.36 +- R²: 0.49 +- Kendall 𝜏: 0.48 +- Spearman ρ: 0.65 + +## System Details +- Ligands: 34 +- Host Atoms: 6680 +- Map Details: + - Edges: 60 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 22 + - Mean Dummy Atoms: 9.6 + - Median Dummy Atoms: 9.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 7.99 Hours +- Average Time Per Edge: 0.13 Hours +- Total Nanoseconds Simulated: 7820.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/p38/ddg_results.csv b/summaries/2026_june_08/jacs_set/p38/ddg_results.csv new file mode 100644 index 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b/summaries/2026_june_08/jacs_set/p38/dg_results.csv new file mode 100644 index 0000000..fc8845e --- /dev/null +++ b/summaries/2026_june_08/jacs_set/p38/dg_results.csv @@ -0,0 +1,35 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2aa,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CO)CO)nc21,-8.940071021262247,0.08292458160536002,-9.27 +2z,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(C)(C)CO)nc21,-10.2659908783789,0.06997133263759414,-10.36 +2y,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCC(C)(C)O)nc21,-9.850309260734138,0.07826330268908177,-9.78 +3flw,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CCO)CCO)nc21,-12.307723417363077,0.06535107283086018,-10.68 +2bb,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCCS(C)(=O)=O)nc21,-9.125859872796603,0.07462478101961072,-9.06 +2v,CNc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-7.781127762338636,0.07089355924522132,-8.97 +3fly,CC(C)Nc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-9.849077264489964,0.049294948747611825,-11.42 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--- /dev/null +++ b/summaries/2026_june_08/jacs_set/ptp1b/README.md @@ -0,0 +1,40 @@ +# Ptp1B Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.29 +- RMSE: 2.14 +- R²: 0.32 +- Kendall 𝜏: 0.53 +- Spearman ρ: 0.65 + +## System Details +- Ligands: 23 +- Host Atoms: 5488 +- Map Details: + - Edges: 40 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 30 + - Mean Dummy Atoms: 11.2 + - Median Dummy Atoms: 11.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.28 Hours +- Average Time Per Edge: 0.13 Hours +- Total Nanoseconds Simulated: 5476.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/ptp1b/ddg_results.csv b/summaries/2026_june_08/jacs_set/ptp1b/ddg_results.csv new file mode 100644 index 0000000..3c19d73 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/ptp1b/ddg_results.csv @@ -0,0 +1,41 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +20667,23485,7.607801715051263,0.04354757563630929,4.90623900569478,0.0420476682507589,0.41000000000000014,2.701562709356482,0.06053426921278522,2.8376898344233545,0.11228224251704268 +20667,23482,-27.510356324413234,0.05779841164921658,-29.595926954952628,0.05920084006891171,1.4100000000000001,2.085570630539393,0.08273690744786849,2.4532366471844647,0.09302848429187997 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/dev/null and b/summaries/2026_june_08/jacs_set/ptp1b/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/ptp1b/dg_results.csv b/summaries/2026_june_08/jacs_set/ptp1b/dg_results.csv new file mode 100644 index 0000000..055a7ea --- /dev/null +++ b/summaries/2026_june_08/jacs_set/ptp1b/dg_results.csv @@ -0,0 +1,24 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +20667,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Br,-13.075582954500444,0.07542433921021503,-11.42 +23485,Cc1c(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc(C(=O)[O-])c1OCC(=O)[O-],-10.23789312007709,0.08317734691223569,-11.01 +23482,CS(=O)(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-10.62234630731598,0.05445611025722438,-10.01 +23486,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Cl,-13.76127886052539,0.07277222368452713,-12.47 +20669,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCc3ccccc3)c2)c1Br,-7.093728934820815,0.07071538446115051,-8.61 +23466,Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-4.483882783100103,0.06958396387810865,-7.85 +23330,CC1(C)CC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC(C)(C)C1,-9.747569344419812,0.07338501841614294,-10.13 +20670,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCC3)c2)c1Br,-8.21780976160664,0.05444637691637699,-9.08 +23475,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCC3)c2)c1Br,-7.652986003832442,0.05529155264508321,-8.72 +23472,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NS(=O)(=O)c3ccc(F)cc3)c2)c1Br,-6.2530802936781065,0.06928152221892415,-8.65 +23467,COc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-5.2318532386418735,0.059311252304939555,-7.34 +23473,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(OCc3ccccc3)c2)c1Br,-8.864197960762926,0.06713930783070346,-8.39 +23468,CCC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.0957429071080025,0.05103161840886576,-7.75 +23469,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC(=O)c3ccccc3)c2)c1Br,-8.199121897336907,0.08366946049569465,-7.72 +23471,COC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.777399472513238,0.06274691499834843,-7.75 +23474,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCC3CCCCC3)c2)c1Br,-8.695256135579845,0.08568193248178502,-9.11 +23470,CC(C)NC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-8.414590874208807,0.06171971080598211,-7.72 +23476,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCCC3)c2)c1Br,-9.055972419117415,0.06606996363241287,-9.41 +23477,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCOCC3)c2)c1Br,-8.294879552972581,0.040843159822173764,-8.85 +23479,CC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-8.800751082000566,0.06482461494476773,-9.14 +23483,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)c4ccccc4)CC3)c2)c1Br,-10.62184815676426,0.06617950998734079,-9.87 +23480,COC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-9.059882997289861,0.06825872772365274,-8.72 +23484,O=C([O-])COc1cc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc1C(=O)[O-],-16.212344941826846,0.07624304852326588,-7.75 diff --git a/summaries/2026_june_08/jacs_set/thrombin/README.md b/summaries/2026_june_08/jacs_set/thrombin/README.md new file mode 100644 index 0000000..4399fe5 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/thrombin/README.md @@ -0,0 +1,40 @@ +# Thrombin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.62 +- RMSE: 0.72 +- R²: 0.85 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.78 + +## System Details +- Ligands: 11 +- Host Atoms: 5256 +- Map Details: + - Edges: 19 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 6 + - Mean Dummy Atoms: 2.9 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.21 Hours +- Average Time Per Edge: 0.06 Hours +- Total Nanoseconds Simulated: 1307.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/thrombin/ddg_results.csv b/summaries/2026_june_08/jacs_set/thrombin/ddg_results.csv new file mode 100644 index 0000000..5f3a718 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/thrombin/ddg_results.csv @@ -0,0 +1,20 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +1a,5,1.8186684426405095,0.03920831541496332,1.5087888968647394,0.04135051187297619,-0.09999999999999964,0.30987954577577015,0.056983829546954766,0.18224236944350114,0.0505341679881835 +1a,3b,1.2700163783958194,0.04037479635798057,3.3078344322646775,0.03959313469663639,-0.3799999999999999,-2.0378180538688584,0.056548567586229746,-1.8581126177820932,0.04341615241396723 +1b,1c,0.023559436601885364,0.02547104300452814,0.34576759478641705,0.025630240914384955,-0.09999999999999964,-0.3222081581845317,0.036134239732806536,-0.4261341434704198,0.04422758584664609 +1b,3b,2.7818072799667704,0.04255501880482185,2.9097378788858315,0.040249706671084004,0.6000000000000005,-0.12793059891906075,0.05857446980201396,-0.32510655573774283,0.041609601497168 +1b,5,1.9058313920611096,0.04381438636217667,0.5653592439272249,0.04358360796779163,0.8800000000000008,1.3404721481338846,0.06179992990112725,1.7152484314878516,0.04899080302034498 +1d,1c,0.220062924446067,0.035785873513781735,0.4106709388843315,0.036134160473805195,-0.3100000000000005,-0.19060801443826447,0.050855740052535764,-0.12208658531725547,0.05227085425599193 +1d,1a,1.3154669501526617,0.06073965581506375,-0.2797661636640514,0.061571475665029685,0.7699999999999996,1.595233113816713,0.08648903054203898,1.8370536201975147,0.049381401482025654 +1d,5,2.5266763156950427,0.045597721768070316,0.2539656033063301,0.04721289275371824,0.6699999999999999,2.2727107123887125,0.06563695203627644,2.019295989641016,0.05635833243990583 +3a,1b,-0.8340103408318666,0.033050876005392416,-1.0147528075887946,0.03448739605145405,-0.14000000000000057,0.18074246675692793,0.04776757154318892,0.0566773565029175,0.04352274964413875 +3a,1c,-1.0777019362290818,0.04072471610983816,-0.5294650503562756,0.04133135284741407,-0.2400000000000002,-0.5482368858728063,0.058023988405006735,-0.3694567869675023,0.04838959064290821 +3a,3b,2.364630420408345,0.04591511177995602,2.6379863701145614,0.04201794337943396,0.45999999999999996,-0.27335594970621646,0.06223909587713477,-0.26842919923482533,0.04600904334496541 +6a,1a,4.71057923008827,0.05141871638046525,0.8727313722305052,0.04975524474521244,1.6999999999999993,3.837847857857765,0.07155046312827552,3.70417038082448,0.04400357644686015 +6a,1b,3.4706401389297694,0.04382420697235527,1.359772737024282,0.044557816632071305,0.7199999999999989,2.1108674019054874,0.062497681075165686,2.1711643187801295,0.04222216700306793 +6a,6b,4.58998494014762,0.036999333324492775,3.6385756884764566,0.03464403068062481,0.28999999999999915,0.9514092516711633,0.05068687727861123,0.5727387529877905,0.04936207235203932 +6a,7a,5.888566158675125,0.04130679014718003,5.0722788490369854,0.04173511664874421,0.9599999999999991,0.8162873096381389,0.0587202765145691,1.361307470708983,0.05207088697222881 +6b,7a,2.599756169987224,0.036481228598914235,1.3024950450739674,0.033636267614759185,0.6699999999999999,1.2972611249132564,0.04962135164561658,0.7885687177211924,0.05559968784007042 +6e,6b,1.871624636876377,0.03649851920560157,1.5456985448910578,0.035552231903214236,0.019999999999999574,0.3259260919853189,0.05095196853411643,0.17222804313541573,0.05579498765471972 +6e,1a,2.489155574970481,0.05072082854497876,-0.7612549212267506,0.04915154700639226,1.4299999999999997,3.2504104961972318,0.070629151357005,3.303659670972105,0.051115371470987346 +6e,7a,3.6701304537790134,0.03932466385857303,2.868178438720861,0.04155439256902874,0.6899999999999995,0.8019520150581525,0.05721185829328314,0.9607967608566081,0.058205186457711736 diff --git a/summaries/2026_june_08/jacs_set/thrombin/dg_plot.png b/summaries/2026_june_08/jacs_set/thrombin/dg_plot.png new file mode 100644 index 0000000..0927a82 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/thrombin/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/thrombin/dg_results.csv b/summaries/2026_june_08/jacs_set/thrombin/dg_results.csv new file mode 100644 index 0000000..82e4768 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/thrombin/dg_results.csv @@ -0,0 +1,12 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(F)c1,-6.421192895964432,0.03013273395478755,-7.48 +5,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1ccccc1,-6.238950526520931,0.04056748055608018,-7.58 +3b,CCc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-8.279305513746525,0.03125668944150717,-7.86 +1b,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(Cl)c1,-7.954198958008782,0.027465948043173382,-8.46 +1c,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(Br)c1,-8.380333101479202,0.03466555996824731,-8.56 +1d,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(I)c1,-8.258246516161947,0.039122131290856316,-8.25 +3a,Cc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-8.0108763145117,0.03376168589801285,-8.32 +6a,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1Cl,-10.125363276788912,0.03206763297352424,-9.18 +6b,Cc1ccc(Cl)cc1CNC(=O)[C@@H]1CCCN1C(=O)[C@H]([NH3+])Cc1ccccc1,-9.552624523801121,0.03752707159322861,-8.89 +7a,Cc1ccc(C)c(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-8.764055806079929,0.041024921517901394,-8.22 +6e,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1F,-9.724852566936537,0.041289218266116645,-8.91 diff --git a/summaries/2026_june_08/jacs_set/tyk2/README.md b/summaries/2026_june_08/jacs_set/tyk2/README.md new file mode 100644 index 0000000..938bef0 --- /dev/null +++ b/summaries/2026_june_08/jacs_set/tyk2/README.md @@ -0,0 +1,40 @@ +# Tyk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.40 +- RMSE: 0.50 +- R²: 0.84 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.84 + +## System Details +- Ligands: 16 +- Host Atoms: 4670 +- Map Details: + - Edges: 28 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 13 + - Mean Dummy Atoms: 6.6 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.54 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 2878.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/jacs_set/tyk2/ddg_results.csv b/summaries/2026_june_08/jacs_set/tyk2/ddg_results.csv new file mode 100644 index 0000000..543b00f --- /dev/null +++ b/summaries/2026_june_08/jacs_set/tyk2/ddg_results.csv @@ -0,0 +1,29 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +ejm_31,ejm_55,-0.3331859195445168,0.04983508305971502,0.3325967812972407,0.04763838327403497,0.3299999999999983,-0.6657827008417575,0.06894164970852198,-0.6998262582801438,0.07328728498242193 +ejm_31,ejm_45,22.010940012832048,0.050621652513578634,22.305600489642536,0.05041546287346862,-0.02000000000000135,-0.2946604768104883,0.07144417820894572,-0.024326688402684482,0.07074868815454798 +ejm_42,ejm_46,25.049254712104528,0.054912470742435396,25.931558937081718,0.056888762241972084,-1.5300000000000011,-0.8823042249771911,0.07906776025955492,-1.2068277598415786,0.062398462836208646 +ejm_42,ejm_48,26.40947157442703,0.06428778643916094,26.513224579125776,0.06615312920755168,0.7799999999999994,-0.10375300469874546,0.09224508653146893,0.10245505603617211,0.07007297342067814 +ejm_42,ejm_54,-11.950895781163736,0.05502417910172033,-11.569808242809684,0.05576034814592301,-0.75,-0.3810875383540513,0.07833821998981555,-0.22952916351237285,0.059758366573720904 +ejm_43,ejm_48,23.784867165807388,0.059653253389068926,24.37433887511579,0.0610652590240326,-0.7400000000000002,-0.589471709308402,0.08536671775096345,-0.5807750058432894,0.07208841644455646 +ejm_43,ejm_50,-14.998431742644364,0.05508518204804686,-14.066545556586606,0.05230020852769602,-0.7200000000000006,-0.9318861860577576,0.07595846952978286,-0.9584398046975622,0.0543200485341178 +ejm_44,ejm_42,-8.157262166146685,0.05212455510107592,-5.846167958254632,0.05147160354507736,-2.3599999999999994,-2.3110942078920527,0.07325500130357462,-2.327083365096282,0.06232782145351903 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+ejm_47,ejm_50,-70.62739436495136,0.06529376722891882,-70.60312844962166,0.06553852908597942,0.7199999999999989,-0.024265915329702036,0.0925125658151259,0.167121058145403,0.0650201689630185 +ejm_49,ejm_31,-18.86615309561109,0.05502823367454576,-17.04524012069284,0.05162555455913894,-1.7899999999999991,-1.8209129749182498,0.07545398852863276,-1.5601615613732562,0.07899020456684168 +ejm_49,ejm_50,-32.85532026814726,0.06696117230506815,-31.317864442149155,0.06619326548171314,-1.2300000000000004,-1.5374558259981084,0.0941559716194442,-1.6160201976634472,0.06694227309855519 +ejm_49,ejm_55,-31.064545115268217,0.06634831558813051,-29.128048211939596,0.06599731109761685,-1.4600000000000009,-1.936496903328623,0.09358281922178763,-2.2599878196534,0.07901681567513566 +ejm_50,ejm_46,37.57337590316014,0.05977878466081697,38.33215639870823,0.05884129269646611,-2.33,-0.75878049554809,0.08387968062478256,-0.931618017023478,0.05549658630392945 +ejm_50,ejm_54,-0.28454881319330505,0.05585142109705766,-0.24622075504008334,0.057750378000897176,-1.549999999999999,-0.03832805815322172,0.08033982448205478,0.045680579305727775,0.05251062085547059 +ejm_50,jmc_27,35.58104754542814,0.06256042504065298,37.89333561985098,0.062149206099298054,-2.299999999999999,-2.3122880744228422,0.08818350526056552,-1.7175932369571374,0.05253881542758102 +ejm_55,ejm_54,-0.36575316682388237,0.05178936066052138,-1.2592883278373248,0.05219483726162558,-1.3199999999999985,0.8935351610134424,0.07352849049445485,0.6896482012956806,0.06722911969127517 +jmc_23,ejm_46,2.7948354211656925,0.03263675471662637,2.1553122483869736,0.032186576236182936,0.3899999999999988,0.639523172778719,0.0458381222154753,0.7054644666251839,0.06873292908808304 +jmc_23,jmc_28,9.130743259290554,0.034207181025428655,8.464910082642486,0.03297272949392734,0.7199999999999989,0.6658331766480676,0.047511389413341217,0.6664833126275749,0.07051247122897776 +jmc_23,jmc_30,-5.1109176769791285,0.035521813930008896,-5.431252187847902,0.034355509290725755,0.7599999999999998,0.32033451086877385,0.0494176110663326,0.24298907385296964,0.07460585630434885 +jmc_27,ejm_46,1.2813499418752674,0.036445089072411556,0.612216957952581,0.03553858871505869,-0.030000000000001137,0.6691329839226865,0.05090418259194532,0.7859752199336594,0.06316443460979412 +jmc_27,jmc_30,-6.270490908247547,0.041001643733193496,-6.589553830385416,0.04010508830155124,0.33999999999999986,0.3190629221378687,0.05735462402020387,0.3234998271614451,0.06950945297909239 +jmc_28,jmc_27,-8.135297893689588,0.035274746759766565,-7.464846631102442,0.03611308752605491,-0.29999999999999893,-0.6704512625871467,0.05048230234082203,-0.7469940659360503,0.06509638129239538 +jmc_28,jmc_30,-14.488554089635183,0.03289499192172119,-13.998188035884809,0.03351482267269536,0.040000000000000924,-0.4903660537503753,0.046960875548825935,-0.42349423877460524,0.07347721467297658 diff --git a/summaries/2026_june_08/jacs_set/tyk2/dg_comparison_plot.png b/summaries/2026_june_08/jacs_set/tyk2/dg_comparison_plot.png new file mode 100644 index 0000000..c5a4a79 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/tyk2/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/tyk2/dg_plot.png b/summaries/2026_june_08/jacs_set/tyk2/dg_plot.png new file mode 100644 index 0000000..4596d95 Binary files /dev/null and b/summaries/2026_june_08/jacs_set/tyk2/dg_plot.png differ diff --git a/summaries/2026_june_08/jacs_set/tyk2/dg_results.csv b/summaries/2026_june_08/jacs_set/tyk2/dg_results.csv new file mode 100644 index 0000000..69bb0ea --- /dev/null +++ b/summaries/2026_june_08/jacs_set/tyk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +ejm_31,CC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.596680352262918,0.05180164764835119,-9.54 +ejm_55,COC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.296506610543062,0.05184221678333979,-9.21 +ejm_45,O=C(CC1CC1)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.621007040665603,0.04818678425155127,-9.56 +ejm_42,CCC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.377329245735009,0.04170039906411209,-9.78 +ejm_46,O=C(Nc1ccnc(NC(=O)C2CC2)c1)c1c(Cl)cccc1Cl,-10.584157005576587,0.04641815250756444,-11.31 +ejm_48,O=C(Nc1ccnc(NC(=O)C2CCCC2)c1)c1c(Cl)cccc1Cl,-9.274874189698837,0.05631428168687641,-9.0 +ejm_54,CCNC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.606858409247382,0.042803493939782576,-10.53 +ejm_43,CC(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-8.694099183855547,0.0450049048835228,-8.26 +ejm_50,O=C(CO)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.65253898855311,0.03041753128006905,-8.98 +ejm_44,CC(C)(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-7.050245880638727,0.046323148047553366,-7.42 +ejm_47,O=C(Nc1ccnc(NC(=O)C2CCC2)c1)c1c(Cl)cccc1Cl,-9.819660046698512,0.05746647860105485,-9.7 +ejm_49,O=C(Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1)c1ccccc1,-8.036518790889662,0.05963255586026451,-7.75 +jmc_27,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2Cl)c1)c1c(Cl)cccc1Cl,-11.370132225510247,0.042838077890580556,-11.28 +jmc_23,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2F)c1)c1c(Cl)cccc1Cl,-11.289621472201771,0.050690932708048884,-11.7 +jmc_28,C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.623138159574196,0.049014670660991654,-10.98 +jmc_30,N#C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-11.046632398348802,0.0547399592262655,-10.94 diff --git a/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/README.md b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/README.md new file mode 100644 index 0000000..ba99737 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/README.md @@ -0,0 +1,40 @@ +# Bace Ciordia Prospective Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.28 +- RMSE: 1.76 +- R²: 0.48 +- Kendall 𝜏: 0.78 +- Spearman ρ: 0.88 + +## System Details +- Ligands: 9 +- Host Atoms: 7184 +- Map Details: + - Edges: 17 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 4.0 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.58 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 1534.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/ddg_results.csv b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/ddg_results.csv new file mode 100644 index 0000000..68f44c6 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/ddg_results.csv @@ -0,0 +1,18 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +spiro10,spiro1,0.4633517774084826,0.04413169800948319,-5.341638709574579,0.04519200277158051,0.9800000000000004,5.804990486983062,0.06316584428080387,5.718051769620546,0.045519151804406494 +spiro10,spiro15,6.992725482722128,0.05579197955166819,2.6848210129122427,0.054571672096746585,-0.5500000000000007,4.307904469809886,0.07804365687055285,4.449042312504215,0.04426347531491864 +spiro10,spiro6,-1.8197472039118228,0.044758005469521835,-3.4840372132822006,0.04591260678313178,-1.0299999999999994,1.6642900093703776,0.06411900276230303,1.6586054518372144,0.05249245205846119 +spiro16,spiro1,-8.897170373639597,0.04821525700033529,-9.571220715530465,0.04610721533378791,0.6600000000000001,0.674050341890869,0.06671271478095211,0.8997916100853356,0.040706833841303365 +spiro16,spiro15,-2.2220008080685427,0.03860620938610218,-1.799171184510953,0.038337223344931004,-0.870000000000001,-0.42282962355758974,0.05440755551357446,-0.36921784703099547,0.03929768933850043 +spiro16,spiro3,0.05616284225528562,0.04998228377882566,-0.04265427101477664,0.04930770374115535,-0.8000000000000007,0.09881711327006226,0.07021024383929031,-0.24049201540148069,0.04729010153525664 +spiro2,spiro1,25.079781341180507,0.046887871654929844,27.363605898713843,0.04618130749046674,-0.4899999999999993,-2.2838245575333382,0.06581174416362336,-2.356139926106458,0.04376674129586754 +spiro2,spiro15,31.93569310079359,0.04920722872993669,35.47399291981461,0.05038578672283118,-2.0200000000000005,-3.53829981902102,0.07042782733379568,-3.625149383222789,0.04245927118570462 +spiro2,spiro3,34.2693626771476,0.04914273953809515,37.93123171702705,0.04921085828637216,-1.9500000000000002,-3.6618690398794524,0.06954651265585116,-3.4964235515932742,0.04994832355035351 +spiro3,spiro15,-1.821958217289619,0.045061113491760854,-1.8270078849114972,0.04281214251785167,-0.07000000000000028,0.005049667621878337,0.06215612195179325,-0.1287258316295148,0.0396418288699413 +spiro4,spiro1,-10.644606828670504,0.05637777982643889,-11.015304157143603,0.05599068656765227,0.10000000000000053,0.3706973284731001,0.07945697603404937,0.8711625962293947,0.04546779664924142 +spiro4,spiro15,-3.1180084071182317,0.057849100876651634,-3.121050730083338,0.058213926492154955,-1.4300000000000006,0.003042322965106484,0.08206935914134482,-0.3978468608869363,0.04421066158856458 +spiro5,spiro1,-9.92946158243027,0.05154602965544337,-10.273969560414342,0.05096709002135537,0.2400000000000011,0.3445079779840732,0.07248887803301131,0.22217516606062748,0.047639879480324436 +spiro5,spiro15,-3.330891902084866,0.05753374567141788,-2.260444252924306,0.058120400440517604,-1.29,-1.0704476491605601,0.08178088308614376,-1.0468342910557036,0.046441578169369384 +spiro5,spiro4,0.09517052622825128,0.03855968282799075,0.8035636582170637,0.038999900342355516,0.14000000000000057,-0.7083931319888124,0.054843790592088965,-0.6489874301687673,0.05685044855298951 +spiro6,spiro1,1.9255087787385932,0.035290710063024235,-2.312366211084375,0.03701169021413133,2.01,4.237874989822968,0.05113999833065371,4.0594463177833315,0.04228911787301484 +spiro6,spiro15,8.24401398602897,0.04907736116818585,5.774592566922285,0.0489284616765605,0.47999999999999865,2.4694214191066837,0.06930066191074373,2.7904368606670005,0.040934478822131755 diff --git a/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_comparison_plot.png b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_comparison_plot.png new file mode 100644 index 0000000..0aa6226 Binary files /dev/null and b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_plot.png b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_plot.png new file mode 100644 index 0000000..22bc25f Binary files /dev/null and b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_plot.png differ diff --git a/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_results.csv b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_results.csv new file mode 100644 index 0000000..d9c7f52 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/bace_ciordia_prospective/dg_results.csv @@ -0,0 +1,10 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +spiro10,COCC#Cc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-12.645409478923222,0.038981285340690765,-8.5 +spiro1,N#Cc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-6.927357709302676,0.023504309693761487,-7.52 +spiro15,N#Cc1cc(Cl)cc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-8.196367166419007,0.020969373861469007,-9.05 +spiro6,CC#Cc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-10.986804027086007,0.035155610025961626,-9.53 +spiro16,N#Cc1cc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)cc(C(F)(F)F)c1,-7.8271493193880115,0.033235429096120164,-8.18 +spiro3,NC1=[NH+][C@@]2(COc3ccc(-c4cc(Cl)cc(Cl)c4)cc32)[C@H](C(F)(F)F)C1,-8.067641334789492,0.03364164020988947,-8.98 +spiro2,NC1=[NH+][C@@]2(COc3ccc(-c4cncnc4)cc32)[C@H](C(F)(F)F)C1,-4.571217783196218,0.036919846552757325,-7.03 +spiro4,COc1cccc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-7.798520305532071,0.03892130467952635,-7.62 +spiro5,COc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-7.149532875363303,0.04143797223223631,-7.760000000000001 diff --git a/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/README.md b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/README.md new file mode 100644 index 0000000..ba14ebe --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/README.md @@ -0,0 +1,40 @@ +# Bace P3 Arg368 In Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.62 +- RMSE: 1.84 +- R²: 0.16 +- Kendall 𝜏: 0.22 +- Spearman ρ: 0.32 + +## System Details +- Ligands: 21 +- Host Atoms: 6894 +- Map Details: + - Edges: 34 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 6.8 + - Median Dummy Atoms: 7.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.77 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 4610.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/ddg_results.csv b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/ddg_results.csv new file mode 100644 index 0000000..acd4e8c --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/ddg_results.csv @@ -0,0 +1,35 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +17a,17b,18.03046538508602,0.07029960660516395,18.873136794147236,0.0701407390078032,-0.6411999999999995,-0.8426714090612141,0.09930638427312503,-1.0798879769474539,0.08730593919681225 +17a,27a,15.428414266393341,0.07367837077229525,14.53108221490569,0.0734102913216425,1.7872000000000003,0.8973320514876527,0.1040075631460916,0.8930847858794397,0.08936512828743808 +17b,17c,-5.645269391675875,0.04268665873542479,-3.6784702795375988,0.04287513277929924,-0.1637000000000004,-1.966799112138276,0.060501469774189444,-1.8612995302701503,0.08927561283281565 +17b,17d,22.97418417332725,0.053290604673643646,22.83854841466439,0.0539832049513704,0.19099999999999895,0.13563575866285774,0.075855619193994,-0.1968787411718136,0.0862420767998796 +17b,17e,25.641561094661864,0.06213349208901099,26.638993822570146,0.059946584962383635,-0.3682999999999996,-0.9974327279082802,0.08633749989331096,-0.9608192741819064,0.08923800288392161 +17c,17d,25.99021516503636,0.05428823471500121,24.383830409339385,0.056106375276649266,0.35469999999999935,1.6063847556969777,0.07807136334889549,1.6644207890983367,0.08891800111822519 +17c,17e,28.656960338318218,0.06426376500208658,27.912527223383407,0.06289299613079698,-0.20459999999999923,0.7444331149348102,0.08991863241037337,0.9004802560882439,0.09182666426923701 +17d,17g,-5.626306678784052,0.0527865303511617,-1.5173483490083708,0.051478972915387895,0.2728999999999999,-4.108958329775681,0.07373264161100805,-4.371356342458126,0.08338632183756176 +17e,27e,13.863901261122868,0.07495695208032661,15.088695690033441,0.07481414638391183,2.59206,-1.2247944289105739,0.10590420749113687,-0.9532423939269403,0.09492484385334192 +17f,17g,-12.461845439450784,0.06382716370213591,-12.558536769572118,0.061823325022806394,0.5183999999999997,0.09669133012133406,0.08885961030262746,-0.8525480451445375,0.08589419408624767 +17f,27f,16.11210984127761,0.07830843165021233,14.839947247722266,0.07679577326706173,2.537470000000001,1.2721625935553458,0.10968045067012594,1.5228145552314611,0.0887395641343071 +17g,27g,15.818560547803862,0.07791503269083985,14.925625912828833,0.07881586278146442,-1.132299999999999,0.8929346349750283,0.11082730956402972,0.34445020062246634,0.08373131807381436 +27a,27b,13.808357175077607,0.06872187640034329,15.078133218993091,0.06758654915178115,-0.8185400000000005,-1.2697760439154846,0.09638795527569921,-1.101047178755687,0.08919020726735297 +27a,27d,35.88184446896846,0.07001023239306031,38.19109371398362,0.07046800750542648,-0.12278000000000056,-2.309249245015159,0.09933364345233266,-2.4923227678015554,0.0789871722108269 +27b,27c,-6.657285150162893,0.05889440308534827,-3.910967967446195,0.05981882210684531,-0.04096000000000011,-2.7463171827166977,0.08394547154569974,-2.3651979682175526,0.09117400419114136 +27b,27d,21.66652618786537,0.05320370379581121,22.858353864894823,0.05216833808763303,0.6957599999999999,-1.1918276770294542,0.07451288208369072,-1.3912755890458683,0.07723242998961123 +27c,27d,26.046814250174975,0.06274447175524758,24.44686706207005,0.06416559922955503,0.73672,1.5999471881049232,0.08974459794512946,0.9739223791716842,0.08122055984611105 +27c,27e,26.539598545962345,0.06219644450117755,27.960559341600792,0.06098779205617508,0.6548600000000011,-1.4209607956384467,0.08710860169050649,-0.4207892839625007,0.09628255220488623 +27d,27e,4.945158530624708,0.0738442741352708,4.680701413540589,0.07198022366732523,-0.08185999999999893,0.26445711708411823,0.10312191533211158,-1.394711663134185,0.08320143665190273 +27d,27f,6.075731290796213,0.05640807816081081,7.354163996484991,0.05534637799002764,0.17735000000000056,-1.2784327056887783,0.07902589979501123,-1.6735224782792795,0.07673105474924712 +27d,27g,-5.636040801449243,0.05171716634996583,-1.4649193592012069,0.05181142781780348,-2.9740199999999994,-4.171121442248036,0.0732058013260527,-3.704434878032812,0.07661008466276993 +27f,27g,-13.859145383137443,0.06210412354038479,-12.153070718044875,0.06163820203655623,-3.15137,-1.7060746650925678,0.08749965777658049,-2.0309123997535323,0.08664774256377998 +8a,17a,-10.018044419832055,0.07286892766126947,-9.382502971183866,0.0717732761283002,-3.1514499999999996,-0.6355414486481882,0.10228041740574072,-0.8912865159567502,0.09566236174064384 +8a,8b,18.97236261277747,0.07042774116362192,20.239947226918563,0.07083566771056699,-0.7230499999999997,-1.2675846141410898,0.0998887308229111,-1.2908771088823396,0.09894678342379318 +8b,8c,-6.01065626500962,0.043758803512322406,-3.816413392147482,0.04355541324247074,0.2046399999999995,-2.1942428728621377,0.061740642267087205,-2.1032520057922923,0.0937642460735441 +8a,8c,12.947196110660311,0.0694439790479609,16.595508369658965,0.06832728351659519,-0.5184100000000003,-3.6483122589986543,0.09742219407697002,-3.394129114674632,0.09777836517305949 +8b,8e,24.73916378339254,0.06103755917075707,26.390431642448323,0.05870045078560578,0.09549999999999947,-1.651267859055782,0.08468368527619118,-1.8391896759715731,0.09834967246077657 +8c,8d,24.55646180810138,0.05618792407970293,23.705354839092333,0.0554658600564367,-0.04092999999999947,0.8511069690090468,0.07895279883694233,1.1668448741480955,0.09309407942986765 +8d,8e,4.471542737324957,0.05115298873769519,4.989166952775337,0.05042196663130383,-0.06821000000000055,-0.5176242154503805,0.07182619978647825,-0.9027825443273763,0.09771096077869877 +8d,8g,-5.387566399105161,0.05368098762015815,-1.6725447833061198,0.04989953363440815,-2.0054099999999995,-3.715021615799041,0.07329128112406688,-3.0419106284664164,0.09792286729947855 +8e,8f,2.5959474676200625,0.05638844441506806,2.489100148842644,0.05399152550198284,0.9549700000000003,0.1068473187774184,0.07806882533753459,-0.507881248896096,0.10497558629889898 +8f,17f,-7.454935143516418,0.07874722650684667,-6.623632405223378,0.07778673153292036,-4.17457,-0.83130273829304,0.11068830690319209,-2.0489134976395977,0.09984753850308338 +8f,8g,-13.738343947413968,0.06194451588403667,-12.118366708218074,0.06142972348609526,-2.8921699999999992,-1.6199772391958953,0.08723952072132099,-1.6312468352429441,0.10517285677708134 +8g,17g,-9.692383227944749,0.0780835619347532,-6.921360537374577,0.07760825264820255,-0.7640000000000011,-2.771022690570171,0.1100912508945451,-1.2702147075411911,0.09203049187771262 diff --git a/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_comparison_plot.png b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_comparison_plot.png new file mode 100644 index 0000000..d527ea5 Binary files /dev/null and b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_plot.png b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_plot.png new file mode 100644 index 0000000..a95a3b4 Binary files /dev/null and b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_plot.png differ diff --git a/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_results.csv b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_results.csv new file mode 100644 index 0000000..130d5e8 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/bace_p3_arg368_in/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17a,Cc1nc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)co1,-7.768500905493694,0.06222231956261564,-10.9413 +17b,CN1C(=O)C[C@@](C)(c2cc(NC(=O)c3ccc(Cl)cn3)ccc2F)[NH+]=C1N,-8.848388882441148,0.06124304015384292,-11.5825 +27a,Cc1nc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)co1,-6.875416119614254,0.06414443936989397,-9.1541 +17c,CN1C(=O)C[C@@](C)(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)[NH+]=C1N,-10.709688412711298,0.06495710183951854,-11.7462 +17d,COc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)cn1,-9.045267623612961,0.060720555362011576,-11.3915 +17e,CN1C(=O)C[C@@](C)(c2cc(NC(=O)c3cnc(OCC(F)(F)F)cn3)ccc2F)[NH+]=C1N,-9.809208156623054,0.06490540186629759,-11.9508 +17g,CC#CCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)cn1,-13.416623966071088,0.05715149014790705,-11.1186 +27e,CN1C(=O)CC[C@@](C)(c2cc(NC(=O)c3cnc(OCC(F)(F)F)cn3)ccc2F)[NH+]=C1N,-10.762450550549994,0.06926770379589436,-9.35874 +17f,COCCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)cn1,-12.56407592092655,0.06412113342416577,-11.637 +27f,COCCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)cn1,-11.041261365695089,0.06134484893735687,-9.09953 +27g,CC#CCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)cn1,-13.072173765448621,0.06119347024194619,-12.2509 +27b,CN1C(=O)CC[C@@](C)(c2cc(NC(=O)c3ccc(Cl)cn3)ccc2F)[NH+]=C1N,-7.976463298369941,0.06197083160903505,-9.97264 +27d,COc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)cn1,-9.36773888741581,0.04609191113183335,-9.27688 +27c,CN1C(=O)CC[C@@](C)(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)[NH+]=C1N,-10.341661266587494,0.06687536968070446,-10.0136 +8a,Cc1nc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)co1,-6.8772143895369435,0.07266134049166405,-7.78985 +8b,CN1C(=O)[C@@](C)(c2cc(NC(=O)c3ccc(Cl)cn3)ccc2F)[NH+]=C1N,-8.168091498419283,0.0671624563865073,-8.5129 +8c,CN1C(=O)[C@@](C)(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)[NH+]=C1N,-10.271343504211575,0.06542887966235274,-8.30826 +8e,CN1C(=O)[C@@](C)(c2cc(NC(=O)c3cnc(OCC(F)(F)F)cn3)ccc2F)[NH+]=C1N,-10.007281174390856,0.07184610306253596,-8.4174 +8d,COc1cnc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)cn1,-9.10449863006348,0.06622363121291275,-8.34919 +8g,CC#CCOc1cnc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)cn1,-12.146409258529896,0.07213403225335052,-10.3546 +8f,COCCOc1cnc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)cn1,-10.515162423286952,0.07653764559695476,-7.46243 diff --git a/summaries/2026_june_08/janssen_bace/ciordia_retro/README.md b/summaries/2026_june_08/janssen_bace/ciordia_retro/README.md new file mode 100644 index 0000000..fa076d6 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/ciordia_retro/README.md @@ -0,0 +1,40 @@ +# Ciordia Retro Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.01 +- RMSE: 1.31 +- R²: 0.62 +- Kendall 𝜏: 0.59 +- Spearman ρ: 0.79 + +## System Details +- Ligands: 32 +- Host Atoms: 7184 +- Map Details: + - Edges: 55 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.71 Hours +- Average Time Per Edge: 0.10 Hours +- Total Nanoseconds Simulated: 5631.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/janssen_bace/ciordia_retro/ddg_results.csv b/summaries/2026_june_08/janssen_bace/ciordia_retro/ddg_results.csv new file mode 100644 index 0000000..49eca45 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/ciordia_retro/ddg_results.csv @@ -0,0 +1,56 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +11,16,1.7046989300704378,0.05060144028111978,0.8392719771828414,0.049935184141907736,1.6456299999999997,0.8654269528875963,0.07109168990683767,1.3059270982390583,0.07397230937860745 +11,15,4.446009954130317,0.05142732754258402,5.538201514785583,0.05041343077925512,0.7859299999999996,-1.092191560655266,0.07201585951099222,-0.8267589860151485,0.07673173427222196 +11,22,9.938754323017768,0.06153158019906176,10.111632584166378,0.057699943435843185,1.09645,-0.1728782611486098,0.08435294206068378,-0.5829499731495975,0.07422126145017724 +11,27,-2.2556106002017233,0.03941555850719655,-1.0782540431422463,0.039851170103323647,-0.9090100000000003,-1.177356557059477,0.05605088769179549,-1.206350220326705,0.06160391732167116 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b/summaries/2026_june_08/janssen_bace/ciordia_retro/dg_results.csv @@ -0,0 +1,33 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccccc4)cc32)[NH+]=C1N,-7.7245512502829285,0.04760967955270488,-8.70337 +16,COc1ccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)cc1,-6.41862415204387,0.05661467095809328,-7.05774 +15,COc1ccccc1-c1ccc2c(c1)[C@@]1(CC(C)(C)O2)[NH+]=C(N)N(C)C1=O,-8.551310236298077,0.06017538913303044,-7.91744 +22,CC(C)Oc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-8.307501223432526,0.056939565015411926,-7.60692 +27,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(F)c4)cc32)[NH+]=C1N,-8.930901470609633,0.03909425843092629,-9.61238 +32,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccccn4)cc32)[NH+]=C1N,-6.647120738070741,0.05469383861969016,-7.721520000000001 +12,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(Cl)c4)cc32)[NH+]=C1N,-10.45756299688739,0.04846343486146958,-10.4569 +24,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(C(F)(F)F)c4)cc32)[NH+]=C1N,-10.503556465542319,0.04442637550001626,-9.78584 +26,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(OC(F)F)c4)cc32)[NH+]=C1N,-10.239080772026433,0.04942026248092858,-10.3651 +40,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccns4)cc32)[NH+]=C1N,-6.405358102650963,0.04994831633366967,-8.64597 +13,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(C#N)c4)cc32)[NH+]=C1N,-9.99092578074233,0.0399161514851024,-9.64326 +14,COc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-10.469060982632875,0.04870459106805738,-9.83624 +21,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cc(Cl)ccc4F)cc32)[NH+]=C1N,-10.141218780920479,0.05038686315543573,-10.2153 +35,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncc(C(F)(F)F)c4)cc32)[NH+]=C1N,-10.362711086230178,0.040948386469067524,-9.88176 +36,CC#Cc1cncc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-14.493087884948974,0.0547780570985548,-10.9787 +18,COc1cc(F)cc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-11.542412083195355,0.06097791371591619,-9.90099 +19,COc1ccc(F)c(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-11.419823534148488,0.06688742825922749,-9.91084 +23,CCOc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-11.791274448427423,0.0631948768603244,-9.81896 +37,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccnc4F)cc32)[NH+]=C1N,-7.156510235032801,0.05344501236659384,-9.45002 +31,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccnc4)cc32)[NH+]=C1N,-7.330960665053356,0.05231904204968787,-9.53354 +33,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccncc4)cc32)[NH+]=C1N,-7.5533158187812015,0.06027123110505947,-7.13992 +17,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cc(Cl)cc(Cl)c4)cc32)[NH+]=C1N,-11.717614788500825,0.05602262373332679,-10.3651 +20,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cc(F)cc(Cl)c4)cc32)[NH+]=C1N,-10.365503345795522,0.04906177956743485,-10.1676 +38,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncc(F)c4)cc32)[NH+]=C1N,-8.963235510688865,0.045597948826034795,-9.38493 +25,CSc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-10.928940663232419,0.06603518367926195,-8.87004 +1a,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(Br)cc32)[NH+]=C1N,-5.172188378158226,0.04457579384392894,-6.08468 +28,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(C4CCCCC4)cc32)[NH+]=C1N,-8.466654761477333,0.059823009764147075,-8.997 +29,CC(C)COc1ccc2c(c1)[C@@]1(CC(C)(C)O2)[NH+]=C(N)N(C)C1=O,-8.490004365439408,0.060096114032450056,-8.73567 +30,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(N4CCCCC4)cc32)[NH+]=C1N,-6.679479329459987,0.05612416974321111,-6.94738 +39,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncnc4)cc32)[NH+]=C1N,-7.270099797453177,0.041668669264145815,-9.36077 +41,Cc1ccc(C(=O)Nc2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)o1,-7.875090197097808,0.06591221309084337,-9.10997 +34,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncc(Cl)c4)cc32)[NH+]=C1N,-10.089570154738091,0.035888155392795454,-10.2494 diff --git a/summaries/2026_june_08/janssen_bace/keranen_p2/README.md b/summaries/2026_june_08/janssen_bace/keranen_p2/README.md new file mode 100644 index 0000000..347e617 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/keranen_p2/README.md @@ -0,0 +1,40 @@ +# Keranen P2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.61 +- RMSE: 0.71 +- R²: 0.08 +- Kendall 𝜏: 0.08 +- Spearman ρ: 0.11 + +## System Details +- Ligands: 12 +- Host Atoms: 6252 +- Map Details: + - Edges: 19 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 8.6 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.04 Hours +- Average Time Per Edge: 0.11 Hours +- Total Nanoseconds Simulated: 1964.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/janssen_bace/keranen_p2/ddg_results.csv b/summaries/2026_june_08/janssen_bace/keranen_p2/ddg_results.csv new file mode 100644 index 0000000..5e5b8f8 --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/keranen_p2/ddg_results.csv @@ -0,0 +1,20 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +29,31,6.630374434423927,0.05215491135044414,6.953186494058336,0.05064314370302058,-0.3699999999999992,-0.32281205963440873,0.07269706171570815,-0.43922909331531557,0.06264370003452642 +29,32,9.303190325455898,0.05639185248750965,10.65656602178246,0.05582462890448632,-0.3699999999999992,-1.3533756963265633,0.0793500486407958,-1.3621425708694233,0.0606752541989988 +29,34,15.352771365085312,0.05894228014756564,16.206342718600503,0.0545024734523477,-0.16000000000000014,-0.8535713535151916,0.08027896362944639,-0.7893332529138366,0.06061558145334403 +29,35,32.890544490531155,0.0673276984269341,31.650193480437462,0.06849522691267564,0.17999999999999972,1.240351010093692,0.09604485975463295,1.3190537262152606,0.07036858340627929 +29,36 out,-2.508240367863191,0.049348829379805774,-3.1671806147048143,0.051528948916007476,-0.3699999999999992,0.6589402468416233,0.07134801705405476,0.6839926577238149,0.05028330094982923 +30,31,2.7103563822090795,0.04316351999150719,3.3006344529482954,0.04158889706701621,0.0,-0.5902780707392157,0.05993935115855118,-0.342516619631569,0.07523727499216569 +30,32,6.0160652040606895,0.05944956731977553,6.973428211078515,0.05683595556810954,0.0,-0.9573630070178258,0.08224704797042047,-1.2654300971856767,0.07360639147753513 +30,34,25.678655448282154,0.06476587505455887,26.174412206977447,0.06489160442276619,0.20999999999999908,-0.49575675869529073,0.09168172607528448,-0.69262077923009,0.07355720977006958 +31,32,3.1859807823377064,0.04272414097227927,4.279335250906593,0.04249922496762577,0.0,-1.0933544685688863,0.060262229834848115,-0.9229134775541077,0.07227096138799201 +33,37 out,-14.367455085241499,0.055863362543744535,-14.30389652463142,0.05584158724928403,-0.3200000000000003,-0.06355856061008033,0.07898732899151129,-0.010189826031647087,0.06652905012982632 +33,35,24.40539649731308,0.07185042404180915,23.114265034964546,0.07110719184325702,0.4299999999999997,1.2911314623485324,0.10108766575018707,0.893711091869255,0.07966518119078567 +33,39 out,-12.029591729318653,0.059862326406038134,-12.249222125953713,0.059075600820417205,0.5600000000000005,0.21963039663505926,0.08410365470677435,0.4342194529352952,0.06820499171535063 +34,39 out,-19.119416723927067,0.06562389238297749,-20.879975490824865,0.06319536611676985,0.47000000000000064,1.7605587668977989,0.09110515655068703,1.6488953401951374,0.06744433467741817 +35,38 out,-31.253249918955937,0.07073031139972322,-30.667181856822513,0.06894803569676622,-0.6799999999999997,-0.586068062133422,0.09877554645328146,-0.8822748269731289,0.07396460114675821 +36 out,28 out,-2.916178497011642,0.03313031147912047,-3.1668965740458077,0.03312001307604667,-0.13000000000000078,0.2507180770341658,0.04684605431475573,0.2272050220966495,0.050883221109468614 +36 out,38 out,1.8857473012397683,0.03904690355642095,2.184227037923899,0.04188230682694094,-0.13000000000000078,-0.2984797366841308,0.05726070469781579,-0.24721375848168314,0.05520357820471096 +37 out,28 out,0.08129974464730838,0.03668215912765221,-0.43034538508528825,0.03439280401215397,0.07000000000000028,0.5116451297325966,0.05028365307020595,0.4960448715061059,0.05560578012838857 +37 out,38 out,4.8632595944372445,0.03968782141923835,4.887700058941669,0.039415194377011804,0.07000000000000028,-0.024440464504424317,0.05593461108100223,0.021626090927773234,0.05958469299925326 +39 out,28 out,-0.109489826707616,0.03528329619213707,-0.12152957459530597,0.033169768182463005,-0.8100000000000005,0.012039747887689972,0.0484266921383281,0.05163559253916361,0.05760042679877291 diff --git a/summaries/2026_june_08/janssen_bace/keranen_p2/dg_comparison_plot.png b/summaries/2026_june_08/janssen_bace/keranen_p2/dg_comparison_plot.png new file mode 100644 index 0000000..dbc85b7 Binary files /dev/null and b/summaries/2026_june_08/janssen_bace/keranen_p2/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/janssen_bace/keranen_p2/dg_plot.png b/summaries/2026_june_08/janssen_bace/keranen_p2/dg_plot.png new file mode 100644 index 0000000..f18d24b Binary files /dev/null and b/summaries/2026_june_08/janssen_bace/keranen_p2/dg_plot.png differ diff --git a/summaries/2026_june_08/janssen_bace/keranen_p2/dg_results.csv b/summaries/2026_june_08/janssen_bace/keranen_p2/dg_results.csv new file mode 100644 index 0000000..d054f6b --- /dev/null +++ b/summaries/2026_june_08/janssen_bace/keranen_p2/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +29,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1OC,-10.434471925180084,0.034515415151669664,-9.99 +31,CCCOc1cc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)ccc1OC,-10.8737010184954,0.05227733037296011,-10.36 +32,CCCCOc1cc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)ccc1OC,-11.796614496049507,0.04990162912191358,-10.36 +34,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1OC1CCCC1,-11.22380517809392,0.04982905610017991,-10.15 +35,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C1CCCC1,-9.115418198964823,0.061322293234307344,-9.81 +36 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1F,-9.750479267456269,0.036566329749087335,-10.36 +30,CCOc1cc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)ccc1OC,-10.53118439886383,0.054108486185839126,-10.36 +33,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1OC(C)C,-10.009129290834078,0.05085388329957048,-10.24 +37 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1Cl,-10.019319116865725,0.042895186962299284,-10.56 +39 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C#N,-9.574909837898783,0.04545111052817867,-9.68 +38 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C(F)(F)F,-9.997693025937952,0.04135623985911497,-10.49 +28 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C,-9.52327424535962,0.03538369284226963,-10.49 diff --git a/summaries/2026_june_08/mcs_docking_set/hne_negative_1/README.md b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/README.md new file mode 100644 index 0000000..c48d3d9 --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/README.md @@ -0,0 +1,40 @@ +# Hne Map Charge -1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.17 +- RMSE: 0.17 +- R²: 1.00 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 2 +- Host Atoms: 3804 +- Map Details: + - Edges: 1 + - Min Dummy Atoms: 10 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 10.0 + - Median Dummy Atoms: 10.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.12 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 102.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/mcs_docking_set/hne_negative_1/ddg_results.csv b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/ddg_results.csv new file mode 100644 index 0000000..aabdd2a --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/ddg_results.csv @@ -0,0 +1,2 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +16,19,-9.463846580125736,0.052465267448811366,-10.110237787583289,0.052212005358210835,0.3026,0.6463912074575527,0.07401822607980511,0.6463912074575529,0.05692824904834691 diff --git a/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_comparison_plot.png b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_comparison_plot.png new file mode 100644 index 0000000..3a2d88b Binary files /dev/null and b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_plot.png b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_plot.png new file mode 100644 index 0000000..3b28f10 Binary files /dev/null and b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_plot.png differ diff --git a/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_results.csv b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_results.csv new file mode 100644 index 0000000..5ca40b1 --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/hne_negative_1/dg_results.csv @@ -0,0 +1,3 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +16,CCOC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N(CC(=O)[O-])[C@@H]1c1ccc(C#N)cc1,-12.010495603728776,0.040254350943162674,-11.8386 +19,CC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N(CC(=O)[O-])[C@@H]1c1ccc(C#N)cc1,-11.364104396271223,0.040254350943162764,-11.536 diff --git a/summaries/2026_june_08/mcs_docking_set/hne_neutral/README.md b/summaries/2026_june_08/mcs_docking_set/hne_neutral/README.md new file mode 100644 index 0000000..219d487 --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/hne_neutral/README.md @@ -0,0 +1,40 @@ +# Hne Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.69 +- RMSE: 0.84 +- R²: 0.82 +- Kendall 𝜏: 0.76 +- Spearman ρ: 0.88 + +## System Details +- Ligands: 14 +- Host Atoms: 3804 +- Map Details: + - Edges: 24 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 25 + - Mean Dummy Atoms: 8.2 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.62 Hours +- Average Time Per Edge: 0.11 Hours +- Total Nanoseconds Simulated: 3078.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/mcs_docking_set/hne_neutral/ddg_results.csv b/summaries/2026_june_08/mcs_docking_set/hne_neutral/ddg_results.csv new file mode 100644 index 0000000..4a5f8d3 --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/hne_neutral/ddg_results.csv @@ -0,0 +1,25 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +14,17,-6.357852801443291,0.04121814422301722,-6.093775037511557,0.04076514318773222,-1.0884999999999998,-0.2640777639317337,0.0579718234343699,-0.26310672856810235,0.07755867545654006 +14,15,-26.25835974960217,0.05837700384139464,-25.60553515580445,0.060744739696868916,-1.9527,-0.6528245937977196,0.08424843012388164,-0.8172097010732546,0.07598928249867225 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a/summaries/2026_june_08/mcs_docking_set/hne_neutral/dg_results.csv b/summaries/2026_june_08/mcs_docking_set/hne_neutral/dg_results.csv new file mode 100644 index 0000000..6e87c3e --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/hne_neutral/dg_results.csv @@ -0,0 +1,15 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +14,CCOC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N[C@@H]1c1ccc(C#N)cc1,-10.284396258348869,0.05017361565358029,-10.3255 +17,CC1=C(C(=O)OCCO)[C@@H](c2ccc(C#N)cc2)NC(=O)N1c1cccc(C(F)(F)F)c1,-10.547502986916971,0.05914352399730432,-11.414 +15,CCOC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N(CC(N)=O)[C@@H]1c1ccc(C#N)cc1,-11.101605959422123,0.05706995134840943,-12.2782 +22,CC1=C(C#N)[C@@H](c2ccc(C#N)cc2)NC(=O)N1c1cccc(C(F)(F)F)c1,-10.60246666969561,0.03609998944254939,-11.3613 +18,CC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N[C@@H]1c1ccc(C#N)cc1,-9.307702486870463,0.04833187291753069,-10.7585 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+6,CCOC(=O)C1=C(N)N(c2cccc([N+](=O)[O-])c2)C2=CCCC(O)=C2[C@@H]1c1ccc(Br)cc1,-7.61488301297515,0.08006820636164041,-7.03256 diff --git a/summaries/2026_june_08/mcs_docking_set/renin/README.md b/summaries/2026_june_08/mcs_docking_set/renin/README.md new file mode 100644 index 0000000..0e41332 --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/renin/README.md @@ -0,0 +1,40 @@ +# Renin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.41 +- RMSE: 1.86 +- R²: 0.26 +- Kendall 𝜏: 0.38 +- Spearman ρ: 0.51 + +## System Details +- Ligands: 29 +- Host Atoms: 5321 +- Map Details: + - Edges: 56 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 24 + - Mean Dummy Atoms: 9.6 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.46 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 6607.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/mcs_docking_set/renin/ddg_results.csv b/summaries/2026_june_08/mcs_docking_set/renin/ddg_results.csv new file mode 100644 index 0000000..6efa503 --- /dev/null +++ b/summaries/2026_june_08/mcs_docking_set/renin/ddg_results.csv @@ -0,0 +1,57 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) 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b/summaries/2026_june_08/mcs_docking_set/renin/dg_results.csv @@ -0,0 +1,30 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +b1a2m,O=C(c1c(Cc2ccccc2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-9.263974428064298,0.0486146446104895,-9.60566 +b1i2c,O=C(c1c(Oc2cccc(C(F)(F)F)c2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-6.721344954932624,0.06560430291594357,-6.88372 +b1i2a,O=C(c1c(Oc2ccccc2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-9.860021382072748,0.03903671264272152,-8.69953 +b1i2h,O=C(c1c(Oc2cccc(F)c2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-10.588417186895732,0.04102211021136991,-9.82353 +b1i1,O=C(c1c(N2CCCCC2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-5.883930258087986,0.08091303089657195,-7.39449 +b1i2e,Cc1ccccc1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-11.29697074527295,0.047224801712460865,-10.4744 +b1i2j,Cc1ccc(F)cc1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-11.518024946096638,0.060038045415091515,-11.3246 +b1i2k,Cc1cccc(F)c1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-10.761168948363999,0.05752593817408117,-10.6355 +b1i2d,COc1ccccc1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-10.371870766520601,0.050702146875784754,-8.41399 +b1i2g,Cc1cccc(Oc2c(C(=O)N3CC[NH2+]CC3)c3ccccc3n2-c2ccccc2)c1,-9.60552142574765,0.04780864817788706,-8.338 +b1i4b,O=C(c1c(Oc2ccccc2)n(-c2ccc(F)cc2)c2ccccc12)N1CC[NH2+]CC1,-9.683375801105893,0.04774509017996362,-8.39094 +b1i4a,O=C(c1c(Oc2ccccc2)n(-c2ccccn2)c2ccccc12)N1CC[NH2+]CC1,-7.846595864378557,0.04780466308384654,-7.23542 +b1i5a,COc1ccc2c(C(=O)N3CC[NH2+]CC3)c(Oc3cc(F)ccc3C)n(-c3ccccc3)c2c1,-13.953447576503354,0.06486135572403672,-10.3953 +b1i2i,Cc1cccc(C)c1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-10.423174950102052,0.06064521113745686,-9.81412 +b1i5b,COc1ccc2c(c1)c(C(=O)N1CC[NH2+]CC1)c(Oc1cc(F)ccc1C)n2-c1ccccc1,-11.798893200627601,0.07045052551619393,-8.00772 +b1i5d,Cc1ccc(F)cc1Oc1c(C(=O)N2CC[NH2+]CC2)c2cc(C(N)=O)ccc2n1-c1ccccc1,-9.679038513149672,0.08105920650911792,-11.2166 +b1i2n,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-9.337797054531078,0.04208906499312622,-10.9765 +b1i2o,O=C(c1c(Cc2c(F)cccc2Cl)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-10.863835681847446,0.0559765165034156,-10.5657 +b1i4e,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1C1CCCCC1,-8.750752190188559,0.06573323705471629,-10.1889 +b1i4g,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1C1CCOCC1,-6.7449362288736525,0.06170170360343455,-8.35437 +b1i4i,COc1ccc(-n2c(Cc3cccc(F)c3C)c(C(=O)N3CC[NH2+]CC3)c3ccccc32)cn1,-7.8033208790651365,0.06127158563954144,-8.7908 +b1i5h,COc1ccc2c(C(=O)N3CC[NH2+]CC3)c(Cc3cccc(F)c3C)n(-c3ccccc3)c2c1,-12.335643026136939,0.05526623365942622,-10.8059 +b1i5n,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccc(OCCO)cc2n1-c1ccccc1,-11.017878324377895,0.06089810789762919,-10.2436 +b1i5o,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccc(S(C)(=O)=O)cc2n1-c1ccccc1,-4.109289766631657,0.06659062043096882,-10.0361 +b1i5c,Cc1ccc(F)cc1Oc1c(C(=O)N2CC[NH2+]CC2)c2cc(O)ccc2n1-c1ccccc1,-12.344014589176155,0.06977211630126989,-11.8676 +b1i5i,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccc(O)cc2n1-c1ccccc1,-12.641844324494377,0.057172298975545745,-11.4568 +b1i5j,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2cc(O)ccc2n1-c1ccccc1,-10.1877202290264,0.05939088482037454,-11.4568 +b1i5l,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2cccc(F)c2n1-c1ccccc1,-8.280321562653372,0.06110789640982516,-9.653 +b1i5k_xray,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2c(C)c(O)ccc2n1-c1ccccc1,-9.244065195074961,0.06009071483864121,-11.8676 diff --git a/summaries/2026_june_08/merck/cdk8/README.md b/summaries/2026_june_08/merck/cdk8/README.md new file mode 100644 index 0000000..48cc33f --- /dev/null +++ b/summaries/2026_june_08/merck/cdk8/README.md @@ -0,0 +1,40 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.89 +- RMSE: 2.16 +- R²: 0.73 +- Kendall 𝜏: 0.68 +- Spearman ρ: 0.86 + +## System Details +- Ligands: 32 +- Host Atoms: 11038 +- Map Details: + - Edges: 57 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 20 + - Mean Dummy Atoms: 10.7 + - Median Dummy Atoms: 10.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 20.08 Hours +- Average Time Per Edge: 0.35 Hours +- Total Nanoseconds Simulated: 8548.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/cdk8/ddg_results.csv b/summaries/2026_june_08/merck/cdk8/ddg_results.csv new file mode 100644 index 0000000..3e194a5 --- /dev/null +++ b/summaries/2026_june_08/merck/cdk8/ddg_results.csv @@ -0,0 +1,58 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +13,42-flipped,14.391929296007191,0.07250230834254534,17.920537914366662,0.07379189302730459,-0.24160000000000004,-3.52860861835947,0.10344964084785738,-3.0035902723225156,0.10694024664990968 +14,16-flipped,5.101732333981254,0.0717907030526204,9.073315712129139,0.0690940996896954,-0.9521699999999989,-3.971583378147884,0.099638846122981,-3.675911372622263,0.15537509541987182 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a/summaries/2026_june_08/merck/cdk8/dg_comparison_plot.png b/summaries/2026_june_08/merck/cdk8/dg_comparison_plot.png new file mode 100644 index 0000000..719935b Binary files /dev/null and b/summaries/2026_june_08/merck/cdk8/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/cdk8/dg_plot.png b/summaries/2026_june_08/merck/cdk8/dg_plot.png new file mode 100644 index 0000000..48fc895 Binary files /dev/null and b/summaries/2026_june_08/merck/cdk8/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/cdk8/dg_results.csv b/summaries/2026_june_08/merck/cdk8/dg_results.csv new file mode 100644 index 0000000..9c935d0 --- /dev/null +++ b/summaries/2026_june_08/merck/cdk8/dg_results.csv @@ -0,0 +1,33 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +13,Cc1cccc(Cc2n[nH]c3cc(O)c(C(=O)N4CC[C@H](O)C4)cc23)c1,-9.504504991469087,0.0787060150013701,-11.2832 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Atoms: 9.8 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.31 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 2438.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/cmet_neutral/ddg_results.csv b/summaries/2026_june_08/merck/cmet_neutral/ddg_results.csv new file mode 100644 index 0000000..f6dc5eb --- /dev/null +++ b/summaries/2026_june_08/merck/cmet_neutral/ddg_results.csv @@ -0,0 +1,20 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL3402744_300,CHEMBL3402745_200,4.946801063008116,0.04661319018855596,6.016217914863968,0.04562764134168088,-0.2402299999999986,-1.0694168518558527,0.06522784032880098,-1.208945537843955,0.07383606496949233 +CHEMBL3402744_300,CHEMBL3402752_30000,23.670851587105794,0.06000718215079682,22.252134386692525,0.06288915330545992,2.7285000000000004,1.4187172004132682,0.08692472325614013,1.197675278631177,0.076323619553019 +CHEMBL3402745_200,CHEMBL3402751_2100,18.62705532977664,0.0631850778615688,17.053830662168593,0.0655498379460988,1.3931599999999982,1.5732246676080457,0.09104468858276317,1.5343546014167222,0.07726596022491196 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new file mode 100644 index 0000000..0fc4f11 Binary files /dev/null and b/summaries/2026_june_08/merck/cmet_neutral/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/cmet_neutral/dg_plot.png b/summaries/2026_june_08/merck/cmet_neutral/dg_plot.png new file mode 100644 index 0000000..5f398e7 Binary files /dev/null and b/summaries/2026_june_08/merck/cmet_neutral/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/cmet_neutral/dg_results.csv b/summaries/2026_june_08/merck/cmet_neutral/dg_results.csv new file mode 100644 index 0000000..d7b8856 --- /dev/null +++ b/summaries/2026_june_08/merck/cmet_neutral/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3402744_300,COC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-6.7587504924858015,0.04985099285432092,-8.89882 +CHEMBL3402745_200,CCOC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-7.967696030329757,0.05446689821917103,-9.13905 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+CHEMBL3402753_200,Cc1ccc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-9.686798396413437,0.05270525082996412,-9.13905 +CHEMBL3402755_4200,Cc1ccc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nn1,-8.356849176601163,0.04884395334377727,-7.33522 diff --git a/summaries/2026_june_08/merck/cmet_positive_1/README.md b/summaries/2026_june_08/merck/cmet_positive_1/README.md new file mode 100644 index 0000000..eb91714 --- /dev/null +++ b/summaries/2026_june_08/merck/cmet_positive_1/README.md @@ -0,0 +1,40 @@ +# Cmet Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.31 +- RMSE: 1.74 +- R²: 0.38 +- Kendall 𝜏: 0.58 +- Spearman ρ: 0.67 + +## System Details +- Ligands: 12 +- Host Atoms: 4977 +- Map Details: + - Edges: 20 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 52 + - Mean Dummy Atoms: 19.8 + - Median Dummy Atoms: 16.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.17 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 3300.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/cmet_positive_1/ddg_results.csv b/summaries/2026_june_08/merck/cmet_positive_1/ddg_results.csv new file mode 100644 index 0000000..63d81a2 --- /dev/null +++ b/summaries/2026_june_08/merck/cmet_positive_1/ddg_results.csv @@ -0,0 +1,21 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL3402741_400,CHEMBL3402763_90,-3.993647697023845,0.06990059632986037,-6.316320719738438,0.0688713749599571,-0.8837799999999998,2.322673022714593,0.09812930070139649,2.5100183738751944,0.10202154801752575 +CHEMBL3402741_400,CHEMBL3402764_90,-10.090975931693396,0.08052512562748407,-15.854343249328261,0.08036424729477254,-0.8837799999999998,5.763367317634865,0.11376602348934169,5.257304550816114,0.08551501109463161 +CHEMBL3402742_23,CHEMBL3402741_400,18.075961793755155,0.07216466898578569,20.129111343722478,0.07350594117558776,1.6921300000000006,-2.053149549967326,0.10300904250567999,-2.261595527416347,0.09024601002575809 +CHEMBL3402742_23,CHEMBL3402756_2.7 redocked,5.172290160379528,0.09382504612897158,6.885664053535976,0.10308631722388747,-1.2691999999999997,-1.7133738931564484,0.1393912769146176,-1.999506328460198,0.0804424053802158 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redocked,2.272927631578447,0.052941758175798714,1.1351063343473116,0.05197784393336124,1.0312000000000001,1.1378212972311355,0.07419249300775387,1.0964287949934075,0.09022003986684206 +CHEMBL3402762_1 redocked,CHEMBL3402757_6.5 redocked,-11.924954389176635,0.08057909821787954,-15.679634795295064,0.08347565733115155,1.109,3.7546804061184282,0.11602231008075348,3.4157236252669314,0.09127008259749768 +CHEMBL3402762_1 redocked,CHEMBL3402759_5.7 redocked,-12.861552827079585,0.08643769607184537,-15.154504729186918,0.08461167009621127,1.0312000000000001,2.2929519021073332,0.12095705857319286,2.5718108454056807,0.08908939043496608 +CHEMBL3402762_1 redocked,CHEMBL3402760_1 redocked,-15.092778648735385,0.0825408434561961,-16.488058768119032,0.07921361344360464,0.0,1.3952801193836482,0.1144018679622544,1.4753820504122732,0.09563303971010388 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b/summaries/2026_june_08/merck/cmet_positive_1/dg_comparison_plot.png new file mode 100644 index 0000000..19d6b60 Binary files /dev/null and b/summaries/2026_june_08/merck/cmet_positive_1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/cmet_positive_1/dg_plot.png b/summaries/2026_june_08/merck/cmet_positive_1/dg_plot.png new file mode 100644 index 0000000..0e731fa Binary files /dev/null and b/summaries/2026_june_08/merck/cmet_positive_1/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/cmet_positive_1/dg_results.csv b/summaries/2026_june_08/merck/cmet_positive_1/dg_results.csv new file mode 100644 index 0000000..7e70c97 --- /dev/null +++ b/summaries/2026_june_08/merck/cmet_positive_1/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3402741_400,CC[NH+](CC)CCCOC(=O)Nc1cccc(CN2N=C(c3ccc(OC)c(OC)c3)CSC2=O)c1,-12.01800093190225,0.06415282502298715,-8.72837 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redocked,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccnc4)ccc3=O)c2)nc1,-10.993839122120688,0.05171751380643491,-10.914 +CHEMBL3402759_5.7 redocked,COc1cccc(-c2ccc(=O)n(Cc3cccc(-c4ncc(OCCC[NH+](C)C)cn4)c3)n2)c1,-12.136492728591493,0.05886805924036434,-11.247 +CHEMBL3402760_1 redocked,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(C#N)c4)ccc3=O)c2)nc1,-13.232921523584901,0.0683681738446152,-12.2782 +CHEMBL3402762_1 redocked,C[N@H+]1CC[C@H](COc2cnc(-c3cccc(Cn4nc(-c5cccc(C#N)c5)ccc4=O)c3)nc2)CC1,-14.708303573997174,0.06686905928265165,-12.2782 diff --git a/summaries/2026_june_08/merck/eg5_neutral/README.md b/summaries/2026_june_08/merck/eg5_neutral/README.md new file mode 100644 index 0000000..e520ef6 --- /dev/null +++ b/summaries/2026_june_08/merck/eg5_neutral/README.md @@ -0,0 +1,40 @@ +# Eg5 Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.88 +- RMSE: 1.09 +- R²: 0.72 +- Kendall 𝜏: 0.54 +- Spearman ρ: 0.74 + +## System Details +- Ligands: 9 +- Host Atoms: 5906 +- Map Details: + - Edges: 15 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 27 + - Mean Dummy Atoms: 11.9 + - Median Dummy Atoms: 8.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.83 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 1848.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/eg5_neutral/ddg_results.csv b/summaries/2026_june_08/merck/eg5_neutral/ddg_results.csv new file mode 100644 index 0000000..652f02d --- /dev/null +++ b/summaries/2026_june_08/merck/eg5_neutral/ddg_results.csv @@ -0,0 +1,16 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL1078691,CHEMBL1084115,5.587733787963827,0.06206497677348273,2.835615051372251,0.060569811757295665,0.7516800000000003,2.752118736591576,0.08672233529032287,2.349949526425652,0.06709876951442563 +CHEMBL1078691,CHEMBL1078998,9.267454450433634,0.06372895322571484,7.918622001493491,0.06146694196995367,-0.18320000000000114,1.3488324489401429,0.08854131484444425,1.7932395556417244,0.06402319764791928 +CHEMBL1078774,CHEMBL1078691,-0.26921902266461517,0.044014102218875514,-0.4406574722522577,0.04309657060917237,0.4131,0.1714384495876425,0.06159996422405619,-0.36596740094442204,0.05690257644349407 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Binary files /dev/null and b/summaries/2026_june_08/merck/eg5_neutral/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/eg5_neutral/dg_plot.png b/summaries/2026_june_08/merck/eg5_neutral/dg_plot.png new file mode 100644 index 0000000..652a979 Binary files /dev/null and b/summaries/2026_june_08/merck/eg5_neutral/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/eg5_neutral/dg_results.csv b/summaries/2026_june_08/merck/eg5_neutral/dg_results.csv new file mode 100644 index 0000000..e374186 --- /dev/null +++ b/summaries/2026_june_08/merck/eg5_neutral/dg_results.csv @@ -0,0 +1,10 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1078691,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)cc1)N2,-12.101309510838103,0.04060946237675764,-10.2494 +CHEMBL1084115,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccsc1)N2,-9.751359984412451,0.05341457138104472,-9.49772 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0000000..d2643cb --- /dev/null +++ b/summaries/2026_june_08/merck/eg5_positive_1/README.md @@ -0,0 +1,40 @@ +# Eg5 Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.87 +- RMSE: 1.02 +- R²: 0.22 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.44 + +## System Details +- Ligands: 19 +- Host Atoms: 5906 +- Map Details: + - Edges: 31 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 36 + - Mean Dummy Atoms: 16.8 + - Median Dummy Atoms: 16.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.08 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 5056.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/eg5_positive_1/ddg_results.csv b/summaries/2026_june_08/merck/eg5_positive_1/ddg_results.csv new file mode 100644 index 0000000..a63eb0c --- /dev/null +++ b/summaries/2026_june_08/merck/eg5_positive_1/ddg_results.csv @@ -0,0 +1,32 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL1077204,CHEMBL1084676,11.56168397640356,0.06106955784882011,11.084817690760019,0.06071301619734155,0.3335000000000008,0.4768662856435413,0.08611365299201423,1.0281216198608174,0.11688260048529583 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Atoms: 1770 +- Map Details: + - Edges: 70 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 4.6 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.04 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 7797.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/hif2a/ddg_results.csv b/summaries/2026_june_08/merck/hif2a/ddg_results.csv new file mode 100644 index 0000000..c31925b --- /dev/null +++ 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b/summaries/2026_june_08/merck/hif2a_jmc2023/README.md @@ -0,0 +1,40 @@ +# Hif2A Jmc2023 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.63 +- RMSE: 1.84 +- R²: 0.58 +- Kendall 𝜏: 0.59 +- Spearman ρ: 0.78 + +## System Details +- Ligands: 38 +- Host Atoms: 1937 +- Map Details: + - Edges: 62 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.8 + - Median Dummy Atoms: 5.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.00 Hours +- Average Time Per Edge: 0.08 Hours +- Total Nanoseconds Simulated: 6562.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 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+35s,CC(F)(F)CCOc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-9.856798644726098,0.06076077946964863,-9.258622958144626 diff --git a/summaries/2026_june_08/merck/pfkfb3/README.md b/summaries/2026_june_08/merck/pfkfb3/README.md new file mode 100644 index 0000000..72808eb --- /dev/null +++ b/summaries/2026_june_08/merck/pfkfb3/README.md @@ -0,0 +1,40 @@ +# Pfkfb3 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.93 +- RMSE: 1.19 +- R²: 0.38 +- Kendall 𝜏: 0.43 +- Spearman ρ: 0.62 + +## System Details +- Ligands: 40 +- Host Atoms: 8158 +- Map Details: + - Edges: 72 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 10.27 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 7917.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/pfkfb3/ddg_results.csv b/summaries/2026_june_08/merck/pfkfb3/ddg_results.csv new file mode 100644 index 0000000..4a2f049 --- /dev/null +++ b/summaries/2026_june_08/merck/pfkfb3/ddg_results.csv @@ -0,0 +1,73 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) 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+39,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(N)c2)c2nccnc2c1,-6.577914407399431,0.06579634448782502,-7.1975 +59,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)OCCO3)c2nccnc2c1,-9.200533788980996,0.07724891211597422,-8.11517 +65,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3scnc3c2)c2nccnc2c1,-8.9204776779062,0.047253785879948954,-9.4879 +67,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)nc3c2)c2nccnc2c1,-10.980536092558122,0.06136008893789654,-10.2436 +68,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)cc3c2)c2nccnc2c1,-10.113402566818056,0.0581795125408887,-9.77823 diff --git a/summaries/2026_june_08/merck/shp2/README.md b/summaries/2026_june_08/merck/shp2/README.md new file mode 100644 index 0000000..791627e --- /dev/null +++ b/summaries/2026_june_08/merck/shp2/README.md @@ -0,0 +1,40 @@ +# Shp2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.66 +- RMSE: 2.09 +- R²: 0.11 +- Kendall 𝜏: 0.16 +- Spearman ρ: 0.23 + +## System Details +- Ligands: 26 +- Host Atoms: 8422 +- Map Details: + - Edges: 46 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 27 + - Mean Dummy Atoms: 7.8 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 7.27 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 5538.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/shp2/ddg_results.csv b/summaries/2026_june_08/merck/shp2/ddg_results.csv new file mode 100644 index 0000000..e1cf36a --- /dev/null +++ b/summaries/2026_june_08/merck/shp2/ddg_results.csv @@ -0,0 +1,47 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,Example 30,-57.65668753122689,0.05263622757532317,-55.68988989832762,0.05256411221959692,-2.00282,-1.966797632899268,0.07438789113018053,-1.8732375683683387,0.060340784915024044 +10,Example 23,-15.654949124458112,0.0557597077546939,-16.0077160523306,0.05752718418186163,-1.5860599999999998,0.3527669278724868,0.08011567842053578,-0.08634411820579935,0.06984577834620476 +11,10,7.185608871130357,0.05379044181366166,8.791250303975637,0.05455274353709515,-0.8001899999999997,-1.6056414328452788,0.0766120973341221,-1.9079476350774005,0.061853504186872396 +11,Example 30,-51.177631419052794,0.05375193956816121,-46.753723883806046,0.05395241393768586,-2.8030099999999996,-4.423907535246752,0.07615861065593735,-3.781185203445739,0.05548739207021287 +3,6,-11.317418669826017,0.07457043165418602,-12.034193616735157,0.07174097826555483,-2.5671,0.7167749469091406,0.10347713389725499,0.7498914673293839,0.09883753695410594 +3,Example 27,91.73137145173934,0.054879500715759075,90.39185920155897,0.05461069864714607,-3.0555900000000005,1.3395122501803587,0.0774214957588679,1.0314786915598626,0.11570281933473561 +4,3,0.7263858350875839,0.04468914748938816,0.3863874859813798,0.04358896163453213,0.3591300000000004,0.33999834910620413,0.06242689708535098,0.430414924687474,0.11347681685374227 +4,SHP836-2,0.0161891044255967,0.052924230292907624,-1.6399868926676804,0.051889188399560825,-0.89114,1.6561759970932772,0.07411789274434236,1.5368184370680957,0.11006724510767817 +4,Example 27,92.02834655137949,0.05931095012356648,90.55606784821968,0.05940741011495858,-2.69646,1.4722787031597981,0.08394658528568671,1.4618936162473366,0.11625657343287456 +7,6,-32.8806535422596,0.05780059154645837,-33.28311102613633,0.05405493929848495,-0.95357,0.4024574838767285,0.07913813774460078,0.4022660465867922,0.0861326307728972 +Example 14,6,-76.39859341584682,0.08194463632070621,-83.37624217458334,0.08210344280975024,1.748190000000001,6.977648758736525,0.11599956354636311,6.145059974432954,0.09695269510379949 +Example 14,Example 27,21.21496597840171,0.07963772461868115,15.474859075015848,0.08151646208958174,1.2597000000000005,5.740106903385862,0.11396096162301858,6.426647198663432,0.11409692712226091 +Example 14,Example 9,-1.7730325853063205,0.0803092507334716,-1.3008299199542384,0.07847661902245874,0.9841300000000004,-0.47220266535208216,0.11228604315126499,-0.3585763408659979,0.09826175607496963 +Example 1,6,-9.016482250082131,0.06084067504056465,-8.925735216487407,0.057098868519135516,0.9581400000000002,-0.09074703359472462,0.08343781232485133,-0.027792972918153858,0.06990299109862443 +Example 1,7,23.83702099290932,0.06948635541142255,24.183703369221938,0.0673756585693314,1.9117100000000002,-0.34668237631262094,0.09678756612299771,-0.43005901950494607,0.07427031927356291 +Example 1,Example 3,-5.3612329536826495,0.07233604129188723,-5.496146647114316,0.07226658415633733,0.7723099999999992,0.1349136934316665,0.10224950882721441,-0.5899307098439834,0.06942968221880846 +Example 1,Example 4,-5.851008271006126,0.07371155589606504,-5.089166647643858,0.07311384466806747,0.7870899999999992,-0.761841623362268,0.10382209665945405,-0.46596425078002834,0.07274632975635185 +Example 1,Example 5,4.466010820544556,0.05170736381692621,3.150104951958309,0.04991278080118052,1.42509,1.3159058685862466,0.07186749724460055,1.3171370972844771,0.063971865986434 +Example 1,Example 8,74.3604847430785,0.0631935275375114,80.75470745344987,0.06334946077019572,-0.7241499999999998,-6.394222710371365,0.08947947307907428,-5.9627482822986595,0.059315061343679476 +Example 22,Example 24,-2.067233010190145,0.04471517620235545,-2.774909840094895,0.04268781785659192,0.1616099999999996,0.7076768299047497,0.06181987363433592,0.7171282102798466,0.08780747678231537 +Example 22,Example 26,3.597057498327615,0.052428968840609005,2.7769290982393273,0.05189440912573339,0.2797800000000006,0.8201284000882881,0.07376873641454454,0.8742917302544404,0.08768925263556566 +Example 22,Example 6,-95.97343176170162,0.06298163649465538,-96.50266509873647,0.06053263798609238,0.16957000000000022,0.5292333370348603,0.08735494718160054,0.43441012891063924,0.08562853972028052 +Example 24,Example 23,2.2593154479418667,0.04321422416694775,4.356725164161207,0.03689168736183915,0.33688000000000073,-2.0974097162193406,0.05681958963909273,-1.8928040760261133,0.08051867035933528 +Example 24,Example 25,8.505814865411317,0.04617728529408304,7.469681332762323,0.03839057308890395,0.20730999999999966,1.0361335326489938,0.06005145942627552,0.8165085884883041,0.08728605815869604 +Example 25,Example 23,-5.753654663291257,0.04728752998470878,-3.0896376239705456,0.04439792526454918,0.12957000000000107,-2.664017039320711,0.06486359733973461,-2.7093126645144174,0.08065016771476169 +Example 26,Example 23,-3.155024977257744,0.04817920429823821,-1.2922835053104735,0.0483535906946942,0.21870999999999974,-1.8627414719472708,0.06825910532582004,-2.049967596000707,0.08038972773521816 +Example 26,Example 25,-0.6750421662161935,0.05943994561118029,-0.9872522693259487,0.058229726087552905,0.08913999999999866,0.3122101031097552,0.08320942335151416,0.6593450685137103,0.0871671268184886 +Example 29,Example 28,10.177447148810813,0.07687507563338365,10.408309833836675,0.07576624846046134,-0.8345700000000003,-0.23086268502586144,0.10793656312580469,-0.6654584855936063,0.09502874372817562 +Example 29,Example 30,-44.79325096956754,0.07230638627436321,-42.097118394837416,0.07123384987482836,-1.5343200000000001,-2.6961325747301212,0.10150110769862074,-2.442158510146739,0.07654603943198124 +Example 2,Example 1,-2.0253714234841564,0.03725564343967952,-0.4582055148514811,0.0328905792106549,-0.7119599999999995,-1.567165908632675,0.04969681246233906,-1.5365655507121252,0.05996886177632799 +Example 2,Example 30,48.04516065708013,0.04611629065462938,52.50944044567597,0.04672503745236841,-0.8808799999999994,-4.464279788595839,0.06565014385869607,-4.604751683091843,0.059593856153738044 +Example 2,Example 4,-7.80052767682755,0.07392564638149403,-5.580146635227494,0.07292691420975915,0.0751299999999997,-2.2203810416000564,0.1038428428399342,-2.0025298014921535,0.07684148924960474 +Example 30,Example 23,41.421975422676475,0.04999803536200227,39.91643334732982,0.050254415959606044,0.41676,1.5055420753466495,0.07088941996871703,1.7868934501625393,0.06427618105756787 +Example 30,Example 3,-56.22789647321764,0.07390946166831278,-58.46609106089745,0.07490798389978687,0.9412299999999991,2.2381945876798066,0.10523219362928117,2.4782554225357343,0.06910603505866053 +Example 30,Example 5,-45.77627660427848,0.05861409782346322,-49.88160416262928,0.05668318700730388,1.59401,4.1053275583508055,0.08153892415873232,4.385323229664195,0.06362046012337824 +Example 4,Example 3,-0.6992103193258791,0.03473017603154295,-0.4649253491553022,0.03330021885369165,-0.014780000000000015,-0.2342849701705769,0.04811537906829501,-0.12396645906395509,0.08443240408962377 +Example 6,Example 28,115.34516027866911,0.0772202127349365,117.30750179105691,0.07394212345448561,0.61191,-1.9623415123877996,0.10691304352504066,-1.6202794202663124,0.08966099299803108 +Example 6,Example 5,9.621407516132068,0.0432023028796396,8.480350746969057,0.041705805564957454,1.50617,1.1410567691630114,0.06004842372557462,0.9883437848447496,0.07759823198469935 +Example 9,7,-46.739768405082046,0.0642821311750311,-52.765890376667166,0.06596598951804333,1.7176300000000007,6.026121971585124,0.09210702558164881,6.101370268712159,0.08760352563057475 +Example 9,Example 8,5.262623369806928,0.05002140858345288,4.694688320016276,0.052315537714170385,-0.9182299999999994,0.5679350497906519,0.07238132910492538,0.568681005918446,0.0753430413516355 +SHP099-1 Example 7,11,14.404462432683477,0.04772498629130167,12.34814776963551,0.04859061731933072,3.398559999999999,2.056314663047967,0.06810816696974434,2.331420055170218,0.06305212904396033 +SHP099-1 Example 7,Example 28,20.397942107446468,0.07356373380195651,20.148977697807922,0.07181022346207824,1.2952999999999992,0.2489644096385447,0.10280238871037352,0.32693487627761186,0.08343794881691918 +SHP099-1 Example 7,Example 29,8.9767952202534,0.0684943765585781,7.866874746615352,0.06780852186301445,2.1298699999999995,1.109920473638048,0.09638192391416142,0.9923933618712182,0.08219499042487402 +SHP099-1 Example 7,Example 8,-10.724638006399676,0.059077400616595103,-6.739056383931642,0.05611877415371403,0.04031999999999947,-3.9855816224680343,0.081482857559914,-4.344327298194463,0.06610718651516832 +SHP836-2,3,0.9851919234286007,0.04340061030773424,1.8214802229453888,0.04352410786272858,1.2502700000000004,-0.8362882995167881,0.06146511970483943,-1.1064035123806217,0.10948219024684709 +SHP836-2,6,-11.16296006212537,0.07085083254070264,-10.328241921061624,0.06773772357203202,-1.3168299999999995,-0.8347181410637461,0.09802162856447402,-0.3565120450512378,0.09490347303176105 diff --git a/summaries/2026_june_08/merck/shp2/dg_comparison_plot.png b/summaries/2026_june_08/merck/shp2/dg_comparison_plot.png new file mode 100644 index 0000000..c5aa7c5 Binary files /dev/null and b/summaries/2026_june_08/merck/shp2/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/shp2/dg_plot.png b/summaries/2026_june_08/merck/shp2/dg_plot.png new file mode 100644 index 0000000..06c8925 Binary files /dev/null and b/summaries/2026_june_08/merck/shp2/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/shp2/dg_results.csv b/summaries/2026_june_08/merck/shp2/dg_results.csv new file mode 100644 index 0000000..788e8c8 --- /dev/null +++ b/summaries/2026_june_08/merck/shp2/dg_results.csv @@ -0,0 +1,27 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)cn2)CC1,-8.484906427838224,0.0468402371129946,-7.15428 +Example 30,CC1([NH3+])CCN(c2nnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-10.358143996206563,0.03803948621313959,-9.1571 +Example 23,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Cl)CC1,-8.571250546044023,0.05181143638218892,-8.74034 +11,CNc1nc(N2CCC(C)([NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-6.5769587927608235,0.040396140501214775,-6.35409 +3,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-8.067642304074383,0.0798390239760948,-5.46294 +6,Nc1nc(N2CCC([NH3+])CC2)ncc1-c1cccc(Cl)c1Cl,-7.317750836744999,0.05826310120220874,-8.03004 +Example 27,C[C@@H]1CN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-7.03616361251452,0.08374289613185723,-8.51853 +4,C[C@@H]1CN(c2ncc(-c3ccc(Cl)c(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-8.498057228761857,0.08063943336731927,-5.82207 +SHP836-2,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-6.961238791693761,0.0749138186971628,-6.71321 +7,C[NH+](C)C1CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-7.720016883331791,0.06343690662509816,-7.07647 +Example 14,Nc1nc(N2CC[C@@H](C[NH3+])C2)cnc1-c1cccc(Cl)c1Cl,-13.462810811177953,0.07749345860259102,-9.77823 +Example 9,Nc1nc(N2CCC(C[NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-13.82138715204395,0.060416360207689965,-8.7941 +Example 1,CC1([NH3+])CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-7.289957863826845,0.03862433433517719,-8.98818 +Example 3,CC1([NH3+])CCN(c2ncc(-c3ccc(Cl)s3)c(N)n2)CC1,-7.879888573670828,0.05769438075037448,-8.21587 +Example 4,Cc1ccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)s1,-7.755922114606873,0.061645675356705565,-8.20109 +Example 5,COc1cc(Cl)c(Cl)c(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1,-5.972820766542368,0.0509956903566441,-7.56309 +Example 8,CC1(C[NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-13.252706146125504,0.04501596716020785,-9.71233 +Example 22,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Br)CC1,-7.395574680297757,0.06254055997852245,-9.23883 +Example 24,Cc1nc(-c2cccc(Cl)c2Cl)c(N)nc1N1CCC(C)([NH3+])CC1,-6.67844647001791,0.0616346601876711,-9.07722 +Example 26,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C(N)=O)CC1,-6.521282950043316,0.0614661157497112,-8.95905 +Example 6,CC1([NH3+])CCN(c2ncc(-c3cc(O)cc(Cl)c3Cl)c(N)n2)CC1,-6.961164551387117,0.05848867558938648,-9.06926 +Example 25,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C#N)CC1,-5.861937881529606,0.061806347671040866,-8.86991 +Example 29,CC1([NH3+])CCN(c2cnc(C3=CCCCC3)c(N)n2)CC1,-7.9159854860598236,0.06642509797781852,-7.62278 +Example 28,CC1([NH3+])CCN(c2cnc(-c3cccc4cc[nH]c34)c(N)n2)CC1,-8.58144397165343,0.06795710774593401,-8.45735 +Example 2,Cc1cccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1Cl,-5.75339231311472,0.045874014211891086,-8.27622 +SHP099-1 Example 7,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-8.908378847931042,0.04841201100535218,-9.75265 diff --git a/summaries/2026_june_08/merck/syk_negative_1/README.md b/summaries/2026_june_08/merck/syk_negative_1/README.md new file mode 100644 index 0000000..2d4456a --- /dev/null +++ b/summaries/2026_june_08/merck/syk_negative_1/README.md @@ -0,0 +1,40 @@ +# Syk Map Charge -1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.85 +- RMSE: 1.18 +- R²: 0.71 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.09 + +## System Details +- Ligands: 6 +- Host Atoms: 4558 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 4 + - Max Dummy Atoms: 25 + - Mean Dummy Atoms: 13.3 + - Median Dummy Atoms: 11.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.67 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 1644.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/syk_negative_1/ddg_results.csv b/summaries/2026_june_08/merck/syk_negative_1/ddg_results.csv new file mode 100644 index 0000000..7c7fe95 --- /dev/null +++ b/summaries/2026_june_08/merck/syk_negative_1/ddg_results.csv @@ -0,0 +1,10 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL3264995,CHEMBL3265001,17.91040952181405,0.0658659804622151,18.12910514829654,0.06687736142621659,0.3435000000000006,-0.2186956264824875,0.09386644157302282,0.014391417872994694,0.07246448820664571 +CHEMBL3264997,CHEMBL3264995,1.5667729796736671,0.07222486222013268,1.4559005946173653,0.07062439217771481,-1.3985000000000003,0.11087238505630181,0.10101601602314761,0.27402551877263015,0.07114984845662155 +CHEMBL3264997,CHEMBL3265001,11.109171729512264,0.07260855935799403,10.361531198356046,0.07241529149918965,-1.0549999999999997,0.7476405311562169,0.10254743943636989,0.28841693664562484,0.07339767368209323 +CHEMBL3265001,redocked CHEMBL3265000 ground state,-33.679820666508164,0.0765164578485521,-33.93289098654834,0.07437114454595499,0.22690000000000055,0.2530703200401683,0.10670443038020765,0.057065883116456106,0.0786478386798168 +docked CHEMBL3264994,CHEMBL3264995,-11.257462626331616,0.07839452456359755,-6.3415368043493086,0.07607004896751755,-2.5765400000000014,-4.915925821982308,0.10923531403109993,-4.791046530640536,0.07768642451193468 +docked CHEMBL3264994,redocked CHEMBL3265000 ground state,-26.589534340196405,0.09034826332731835,-21.852355456404222,0.08819149244897935,-2.0061400000000003,-4.737178883792182,0.12625588313675068,-4.719589229651085,0.08348389683887497 +docked CHEMBL3264998,CHEMBL3264997,-0.5764859228460872,0.0739155469601203,-0.6561687087113763,0.07366988846577045,0.729099999999999,0.07968278586528911,0.10435880676288325,-0.22177744370429586,0.0746431221429499 +docked CHEMBL3264998,docked CHEMBL3264994,10.286517202114252,0.0866425236468669,5.6168597649096945,0.08661310231769813,1.90714,4.669657437204557,0.12251022976467695,4.84329460570887,0.08089793137834646 +docked CHEMBL3264998,redocked CHEMBL3265000 ground state,-22.52570338011844,0.08061414410183394,-22.4462337610113,0.07817971466433497,-0.0990000000000002,-0.0794696191071409,0.11229740876025628,0.12370537605778509,0.07981140087926528 diff --git a/summaries/2026_june_08/merck/syk_negative_1/dg_comparison_plot.png b/summaries/2026_june_08/merck/syk_negative_1/dg_comparison_plot.png new file mode 100644 index 0000000..a9f0782 Binary files /dev/null and b/summaries/2026_june_08/merck/syk_negative_1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/syk_negative_1/dg_plot.png b/summaries/2026_june_08/merck/syk_negative_1/dg_plot.png new file mode 100644 index 0000000..a7bb937 Binary files /dev/null and b/summaries/2026_june_08/merck/syk_negative_1/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/syk_negative_1/dg_results.csv b/summaries/2026_june_08/merck/syk_negative_1/dg_results.csv new file mode 100644 index 0000000..df2693c --- /dev/null +++ b/summaries/2026_june_08/merck/syk_negative_1/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3264995,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-12.213546942610336,0.049629550091191965,-12.3815 +CHEMBL3265001,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5nnn[n-]5)cc4)c3)cn3ccnc23)cc1OC,-12.19915552473734,0.05280160801336416,-12.038 +CHEMBL3264997,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4cccc(C(=O)[O-])c4)c3)cn3ccnc23)cc1OC,-12.487572461382966,0.05098243514335185,-10.983 +redocked CHEMBL3265000 ground state,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(/C([O-])=N/S(C)(=O)=O)cc4)c3)cn3ccnc23)cc1OC,-12.142089641620885,0.058287843674384845,-11.8111 +docked CHEMBL3264994,CC(C)(C)c1ccc(Nc2nc(-c3cccc(NC(=O)c4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1,-7.4225004119698,0.05976694999072977,-9.80496 +docked CHEMBL3264998,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(CC(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-12.26579501767867,0.05451960188869009,-11.7121 diff --git a/summaries/2026_june_08/merck/syk_neutral/README.md b/summaries/2026_june_08/merck/syk_neutral/README.md new file mode 100644 index 0000000..bec32c6 --- /dev/null +++ b/summaries/2026_june_08/merck/syk_neutral/README.md @@ -0,0 +1,40 @@ +# Syk Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.19 +- RMSE: 1.45 +- R²: 0.03 +- Kendall 𝜏: 0.03 +- Spearman ρ: 0.01 + +## System Details +- Ligands: 40 +- Host Atoms: 4558 +- Map Details: + - Edges: 66 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 42 + - Mean Dummy Atoms: 10.0 + - Median Dummy Atoms: 7.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 8.32 Hours +- Average Time Per Edge: 0.13 Hours +- Total Nanoseconds Simulated: 8486.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/syk_neutral/ddg_results.csv b/summaries/2026_june_08/merck/syk_neutral/ddg_results.csv new file mode 100644 index 0000000..ffd00ba --- /dev/null +++ b/summaries/2026_june_08/merck/syk_neutral/ddg_results.csv @@ -0,0 +1,67 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL3259820,CHEMBL3265015 flip,8.451559115922286,0.05912160544068309,6.413921889280419,0.05832704303892531,1.0983799999999988,2.0376372266418668,0.08305063623807137,2.539489357280516,0.08036683971123512 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adjust,-44.933818905581155,0.06178046366766014,-45.3673646655612,0.06041551645450876,-0.5564999999999998,0.4335457599800429,0.0864109965192862,0.38101471094776684,0.12338463188336131 +intermediate_1,docked CHEMBL3264999 adjust,-21.484260980238655,0.05353826200549077,-21.051470453272845,0.05416998007875591,,-0.43279052696580855,0.07616253830001589,-0.8510483257677173,0.11120758598847222 +intermediate,intermediate_1,6.447953858313015,0.08734653751524038,7.896497709658612,0.08662412551353242,,-1.4485438513455964,0.12301689614392615,-1.9033409204506686,0.09572645407348246 diff --git a/summaries/2026_june_08/merck/syk_neutral/dg_comparison_plot.png b/summaries/2026_june_08/merck/syk_neutral/dg_comparison_plot.png new file mode 100644 index 0000000..b9504f7 Binary files /dev/null and b/summaries/2026_june_08/merck/syk_neutral/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/syk_neutral/dg_plot.png b/summaries/2026_june_08/merck/syk_neutral/dg_plot.png new file mode 100644 index 0000000..415cdeb Binary files /dev/null and b/summaries/2026_june_08/merck/syk_neutral/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/syk_neutral/dg_results.csv b/summaries/2026_june_08/merck/syk_neutral/dg_results.csv new file mode 100644 index 0000000..9de0a65 --- /dev/null +++ b/summaries/2026_june_08/merck/syk_neutral/dg_results.csv @@ -0,0 +1,41 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3259820,COc1ccc(Nc2nc(-c3ccc(C(N)=O)cc3)cn3ccnc23)cc1OC,-10.569483764656866,0.056523232839218646,-10.5757 +CHEMBL3265015 flip,COc1ccc(Nc2nc(-c3ccc(C(N)=O)cc3C)cn3ccnc23)cc1OC,-8.02999440737635,0.057131016747252385,-9.47732 +CHEMBL3264996,COC(=O)c1ccc(NC(=O)c2cccc(-c3cn4ccnc4c(Nc4ccc(OC)c(OC)c4)n3)c2)cc1,-12.658836455483812,0.08421295256844388,-10.6659 +CHEMBL3265003 tautomer 2,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5ccn[nH]5)cc4)c3)cn3ccnc23)cc1OC,-14.203237323885872,0.07937474582962051,-10.821 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+CHEMBL3265036,c1cn2cc(-c3ccc4cn[nH]c4c3)nc(Nc3ccc(N4CCCOCC4)cc3)c2n1,-9.681116209801162,0.07229809096282891,-10.4179 +docked CHEMBL3264999 adjust,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(N)=O)cc4)c3)cn3ccnc23)cc1OC,-12.216894553198753,0.08628076496663589,-11.414 +intermediate_1,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccccc4)c3)cn3ccnc23)cc1OC,-11.365846227431035,0.07016236012389819, +intermediate,COc1ccc(Nc2nc(-c3ccccc3)cn3ccnc23)cc1OC,-9.462505306980367,0.06512140378805549, diff --git a/summaries/2026_june_08/merck/tnks2_neutral/README.md b/summaries/2026_june_08/merck/tnks2_neutral/README.md new file mode 100644 index 0000000..39b775e --- /dev/null +++ b/summaries/2026_june_08/merck/tnks2_neutral/README.md @@ -0,0 +1,40 @@ +# Tnks2 Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.57 +- RMSE: 0.80 +- R²: 0.60 +- Kendall 𝜏: 0.55 +- Spearman ρ: 0.73 + +## System Details +- Ligands: 21 +- Host Atoms: 4097 +- Map Details: + - Edges: 33 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 14 + - Mean Dummy Atoms: 4.5 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.36 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 2700.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/tnks2_neutral/ddg_results.csv b/summaries/2026_june_08/merck/tnks2_neutral/ddg_results.csv new file mode 100644 index 0000000..994df24 --- /dev/null +++ b/summaries/2026_june_08/merck/tnks2_neutral/ddg_results.csv @@ -0,0 +1,34 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +1a,1b,-0.9873124969343665,0.049290091660935086,1.0730631609660344,0.0506467224145034,-1.3866099999999992,-2.0603756579004013,0.07067250969984824,-2.2450517996135204,0.07473747925642371 +1a,3a,4.801728424110412,0.05492218883154506,9.57770450408994,0.056475226960295256,-2.4459399999999984,-4.775976079979527,0.07877752272231435,-4.6649116832670625,0.07578110037390047 +1a,5a,-7.046872199580738,0.05362093585436919,-2.8677154892481984,0.05467380070977194,-2.207939999999999,-4.17915671033254,0.07657956154190382,-4.067271915552036,0.07176918297381733 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a/summaries/2026_june_08/merck/tnks2_neutral/dg_comparison_plot.png b/summaries/2026_june_08/merck/tnks2_neutral/dg_comparison_plot.png new file mode 100644 index 0000000..594c985 Binary files /dev/null and b/summaries/2026_june_08/merck/tnks2_neutral/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/tnks2_neutral/dg_plot.png b/summaries/2026_june_08/merck/tnks2_neutral/dg_plot.png new file mode 100644 index 0000000..eb9aea0 Binary files /dev/null and b/summaries/2026_june_08/merck/tnks2_neutral/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/tnks2_neutral/dg_results.csv b/summaries/2026_june_08/merck/tnks2_neutral/dg_results.csv new file mode 100644 index 0000000..72840c7 --- /dev/null +++ b/summaries/2026_june_08/merck/tnks2_neutral/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a,O=c1[nH]c(-c2ccccc2)nc2ccccc12,-6.469639172316706,0.05358830762590543,-8.55056 +1b,COc1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-8.714690971930226,0.052095912425023226,-9.93717 +3a,CC(C)(C)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-11.134550855583768,0.0535823521289473,-10.9965 +5a,CC(C)(O)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-10.536911087868742,0.047740013725601264,-10.7585 +5b,CC(C)(O)c1ccc(-c2nc3cccc(F)c3c(=O)[nH]2)cc1,-11.293077117775859,0.048435030329844864,-10.4744 +3b,CC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-11.6850364754151,0.04866018192073793,-11.5193 +5d,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.850798518228476,0.04690425595146824,-10.8851 +7,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)nc1,-8.509595210664612,0.048090325032920184,-8.39681 +5c,CC(C)(O)c1ccc(-c2nc3cccc(Cl)c3c(=O)[nH]2)cc1,-10.577713931669813,0.05028085733146007,-9.96041 +5j,CC(C)(O)c1ccc(-c2nc3ccc(F)c(F)c3c(=O)[nH]2)cc1,-11.63826294186619,0.04287540277147627,-11.0844 +5n,CC(C)(OCCO)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.834062307874595,0.05721017012441393,-10.7146 +5e,CC(C)(O)c1ccc(-c2nc3ccc(Cl)cc3c(=O)[nH]2)cc1,-10.02665029653818,0.03859011364805401,-10.1076 +5k,CC(C)(O)c1ccc(-c2nc3c(F)cc(F)cc3c(=O)[nH]2)cc1,-10.83532007627161,0.04101108224977582,-10.9634 +5p,COCCOC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-11.173093310479725,0.059333713567255225,-10.5033 +5f,CC(C)(O)c1ccc(-c2nc3c(F)cccc3c(=O)[nH]2)cc1,-10.877473344141618,0.03420290298527276,-10.2631 +5g,CC(C)(O)c1ccc(-c2nc3c(Cl)cccc3c(=O)[nH]2)cc1,-11.47308381328544,0.04901806174938883,-10.806 +5h,COc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-10.036272224797683,0.05165355347550838,-10.0498 +5i,Cc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.607430845784897,0.04726264650238807,-12.0789 +5l,CC(C)(O)c1ccc(-c2nc3c(F)ccc(F)c3c(=O)[nH]2)cc1,-11.568489414850827,0.04274966843556125,-10.0926 +5m,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.110172202862621,0.04535064898098127,-12.6889 +5o_adjust,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)OCCO)cc3)nc12,-11.91702587979331,0.05233081062895989,-12.038 diff --git a/summaries/2026_june_08/merck/tnks2_positive_1/README.md b/summaries/2026_june_08/merck/tnks2_positive_1/README.md new file mode 100644 index 0000000..8e3234d --- /dev/null +++ b/summaries/2026_june_08/merck/tnks2_positive_1/README.md @@ -0,0 +1,40 @@ +# Tnks2 Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.60 +- RMSE: 0.68 +- R²: 0.45 +- Kendall 𝜏: 0.47 +- Spearman ρ: 0.66 + +## System Details +- Ligands: 6 +- Host Atoms: 4097 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.75 Hours +- Average Time Per Edge: 0.08 Hours +- Total Nanoseconds Simulated: 826.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/merck/tnks2_positive_1/ddg_results.csv b/summaries/2026_june_08/merck/tnks2_positive_1/ddg_results.csv new file mode 100644 index 0000000..c09140c --- /dev/null +++ b/summaries/2026_june_08/merck/tnks2_positive_1/ddg_results.csv @@ -0,0 +1,10 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +8b,8a,0.24135344715957177,0.04423780747428374,-0.3931516720971973,0.045020512784665484,1.1240000000000006,0.6345051192567691,0.06311759011183826,0.7695834766510838,0.04728943997597149 +8c_adjust,8a,16.144584027150163,0.06405389807888623,15.56118166129004,0.0647252803213387,-0.6829999999999998,0.5834023658601228,0.09106186782499148,0.502800348384655,0.04815573450512664 +8c_adjust,8d,-0.8773023744416394,0.03472156807580903,-0.11546014032078795,0.03414670862662478,-2.3665000000000003,-0.7618422341208514,0.04869892195598021,-0.7120468517530956,0.047547840684091264 +8c_adjust,8e,13.431143822354105,0.054366663368879485,13.550306160943132,0.053641296034431935,-0.12060000000000137,-0.11916233858902588,0.07637488282229064,-0.18493967202132922,0.047921053179619026 +8d,8b,16.256118508965155,0.060373738445897294,15.689762830881053,0.06102431516246822,0.5594999999999999,0.5663556780841011,0.08584261957199271,0.44526372348666676,0.04667026377933265 +8d,8f,13.239229092718846,0.054376131187740546,13.553406373829338,0.054683584317950215,0.6783999999999999,-0.31417728111049287,0.07711717082987901,-0.0915825599347233,0.04645832909480252 +8e,8a,2.628283507658151,0.05469237346553657,1.7970604963335295,0.054231915284156045,-0.5623999999999985,0.8312230113246215,0.0770217914014054,0.6877400204059843,0.04754447858727825 +8f,8b,2.3859969258260563,0.04946437347240558,2.0925941371064045,0.04888068408749795,-0.1189,0.2934027887196519,0.0695416818884861,0.5368462834213901,0.04658132904404912 +8f,8e,0.8312727502434654,0.036632005347515005,0.1828099949425071,0.03105312130416506,1.567499999999999,0.6484627553009582,0.04802291284909276,0.6186897396664897,0.04684022338124707 diff --git a/summaries/2026_june_08/merck/tnks2_positive_1/dg_comparison_plot.png b/summaries/2026_june_08/merck/tnks2_positive_1/dg_comparison_plot.png new file mode 100644 index 0000000..1637b27 Binary files /dev/null and b/summaries/2026_june_08/merck/tnks2_positive_1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/merck/tnks2_positive_1/dg_plot.png b/summaries/2026_june_08/merck/tnks2_positive_1/dg_plot.png new file mode 100644 index 0000000..f787a52 Binary files /dev/null and b/summaries/2026_june_08/merck/tnks2_positive_1/dg_plot.png differ diff --git a/summaries/2026_june_08/merck/tnks2_positive_1/dg_results.csv b/summaries/2026_june_08/merck/tnks2_positive_1/dg_results.csv new file mode 100644 index 0000000..8064c21 --- /dev/null +++ b/summaries/2026_june_08/merck/tnks2_positive_1/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +8b,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(N4CC[NH+](C)CC4)cc3)nc12,-11.256550009042426,0.03308744017343658,-11.93 +8a,C[NH+]1CCN(c2ccc(-c3nc4ccc(F)cc4c(=O)[nH]3)cc2)CC1,-10.486966532391342,0.033786275852929766,-10.806 +8c_adjust,O=c1[nH]c(-c2ccc(C3CC[NH2+]CC3)cc2)nc2c(F)cc(F)cc12,-10.989766880775997,0.03431417097523966,-10.123 +8d,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C4CC[NH2+]CC4)cc3)nc12,-11.701813732529093,0.03291405207509012,-12.4895 +8e,C[N@H+]1CC[C@H](c2ccc(-c3nc4c(F)cc(F)cc4c(=O)[nH]3)cc2)CC1,-11.174706552797327,0.03345093433860846,-10.2436 +8f,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc([C@H]4CC[N@H+](C)CC4)cc3)nc12,-11.793396292463816,0.032787825763219335,-11.8111 diff --git a/summaries/2026_june_08/miscellaneous_set/btk/README.md b/summaries/2026_june_08/miscellaneous_set/btk/README.md new file mode 100644 index 0000000..c553836 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/btk/README.md @@ -0,0 +1,40 @@ +# Btk Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.80 +- RMSE: 2.19 +- R²: 0.71 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 6 +- Host Atoms: 5400 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 10.9 + - Median Dummy Atoms: 11.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.37 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 1503.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/miscellaneous_set/btk/ddg_results.csv b/summaries/2026_june_08/miscellaneous_set/btk/ddg_results.csv new file mode 100644 index 0000000..abaf1eb --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/btk/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,11,-0.5640968024740275,0.043416627672772226,2.244802628594217,0.046540821799905284,-0.6547000000000001,-2.8088994310682445,0.06364787233118378,-2.519394867185328,0.05397647524984041 +2,10,13.849858606379483,0.06676429730770382,18.937103359285434,0.06631164944620367,-3.182170000000002,-5.087244752905951,0.09409944870862778,-5.443405679034528,0.05307730841366308 +2,7,8.780870787462765,0.06059638792153565,7.8451436705948705,0.06018393419792877,-1.3966800000000008,0.9357271168678938,0.0854050827801124,1.52664163749008,0.06369818568379376 +2,8,14.494123262169927,0.06541974892362283,16.02798155575116,0.06271384576838838,-1.9184600000000005,-1.5338582935812348,0.09062433448192078,-1.8688628128395521,0.06442641251368479 +7,10,-10.473608133957073,0.0713512209057698,-2.9099143871716606,0.0708300215276778,-1.7854900000000011,-7.563693746785413,0.10053799617236889,-6.970047316524608,0.054797065020469625 +7,9 flip,24.110771035036546,0.07605290110324095,28.00019344553663,0.07515904240170211,0.7537000000000003,-3.8894224105000847,0.10692485876053427,-3.634668633539917,0.06924952893639334 +8,10,28.21403900645597,0.0660918213327481,32.05809465193859,0.06367269462257102,-1.2637100000000014,-3.8440556454826207,0.09177331250194187,-3.5745428661949763,0.05564190960808217 +8,11,28.731541115489268,0.059285620736387226,34.31274316663348,0.059407183349457625,-1.9184100000000015,-5.58120205114421,0.08392853066517263,-6.093937733380304,0.06516917861490204 +9 flip,10,-5.891294632106329,0.07833146213702998,-2.3036363724883215,0.07682883530323815,-2.5391900000000014,-3.587658259618008,0.10972004326729484,-3.3353786829846914,0.059625825503253356 +9 flip,11,-5.865767946935017,0.0817659982625658,0.006318983936950351,0.07979608873922142,-3.1938900000000015,-5.8720869308719665,0.11425013894937552,-5.8547735501700195,0.06860203206503024 diff --git a/summaries/2026_june_08/miscellaneous_set/btk/dg_comparison_plot.png b/summaries/2026_june_08/miscellaneous_set/btk/dg_comparison_plot.png new file mode 100644 index 0000000..1f2631d Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/btk/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/btk/dg_plot.png b/summaries/2026_june_08/miscellaneous_set/btk/dg_plot.png new file mode 100644 index 0000000..efd4190 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/btk/dg_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/btk/dg_results.csv b/summaries/2026_june_08/miscellaneous_set/btk/dg_results.csv new file mode 100644 index 0000000..db5ffdd --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/btk/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,NC(=O)c1nnc2c(-c3ccc4cn[nH]c4c3)cccc2c1N,-12.318119946258912,0.02968551956669797,-10.8701 +11,Cc1cc2cn[nH]c2cc1-c1cccc2c(N)c(C(N)=O)nnc12,-14.83751481344424,0.045080259631592914,-11.5248 +2,NC(=O)c1nnc2ccccc2c1N,-6.874714267224384,0.04399966586798474,-7.687929999999999 +7,Cn1cc(-c2cccc3c(N)c(C(N)=O)nnc23)cn1,-5.348072629734304,0.04605961639997415,-9.08461 +8,Cc1ccncc1-c1cccc2c(N)c(C(N)=O)nnc12,-8.743577080063936,0.04706157703359694,-9.60639 +9 flip,NC(=O)c1nnc2c(-c3ccc4cc[nH]c4c3)cccc2c1N,-8.982741263274221,0.051710820869520245,-8.33091 diff --git a/summaries/2026_june_08/miscellaneous_set/cdk8/README.md b/summaries/2026_june_08/miscellaneous_set/cdk8/README.md new file mode 100644 index 0000000..f7c135b --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/cdk8/README.md @@ -0,0 +1,40 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.55 +- RMSE: 1.82 +- R²: 0.01 +- Kendall 𝜏: 0.11 +- Spearman ρ: 0.14 + +## System Details +- Ligands: 10 +- Host Atoms: 11038 +- Map Details: + - Edges: 16 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 1 +- Batch Mode: True +- Total Wallclock Time: 3.37 Hours +- Average Time Per Edge: 0.21 Hours +- Total Nanoseconds Simulated: 1518.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/miscellaneous_set/cdk8/ddg_results.csv b/summaries/2026_june_08/miscellaneous_set/cdk8/ddg_results.csv new file mode 100644 index 0000000..4a1b642 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/cdk8/ddg_results.csv @@ -0,0 +1,17 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +12,14,-5.881134793189315,0.03736163528138732,-6.384357781069106,0.038183141946127194,-1.1986399999999993,0.5032229878797909,0.05342138260825438,0.6970636406412432,0.04980321504179454 +12,15,4.817362993961266,0.04842726669225746,5.44753062596796,0.04520130229588609,0.11278000000000077,-0.630167632006693,0.06624468196411774,-0.8021040370604826,0.05841503279901814 +12,22,-7.279437749027316,0.05010656387307151,-6.5530734333886125,0.05077404993777131,-1.4571400000000008,-0.7263643156387034,0.07133492756181568,-0.8726255964519165,0.05493906626571838 +13,19,21.96053693789259,0.046156631094605785,20.819431149323375,0.046400541934751335,0.9724000000000004,1.1411057885692162,0.0654480319478145,0.5322199804688221,0.05974314119927852 +13,20,24.608093158465454,0.051723059786428625,25.24833083921291,0.05190525106425201,0.9141000000000012,-0.6402376807474572,0.07327639457365177,0.06272227105384509,0.06422947332916687 +13,21,31.778794154619654,0.05292107967246763,28.793906288770874,0.049345378426318844,1.3348600000000008,2.984887865848778,0.07235749474474831,3.043682221865195,0.06359194372853907 +14,17,13.747046413677111,0.04737203936460261,11.079360928182755,0.04363163318821357,0.6362999999999985,2.6676854854943564,0.06440364530236063,2.9864380196275206,0.05801268265896577 +14,19,8.3217852571952,0.05315108710530386,11.106906466099101,0.04866660386375452,0.8067999999999991,-2.7851212089039015,0.07206577823146854,-1.9358114096112136,0.04955257936398918 +14,20,15.297454615916829,0.049012163258097825,16.923010218544363,0.04603459104529539,0.7484999999999999,-1.6255556026275348,0.06724117577753995,-2.4053091190261906,0.05487841511386488 +15,21,33.238241336634296,0.064303067418283,30.909274052269737,0.06047720460279512,-0.1421600000000005,2.3289672843645586,0.08827443999238166,2.074818509486885,0.06214584730174923 +15,22,-12.36208088398871,0.05632261033928117,-12.332501817076185,0.0553549972088545,-1.5699200000000015,-0.029579066912525334,0.07897095764534448,-0.0705215593914339,0.058397973623900534 +16,17,30.32418135188093,0.0538920408304574,29.214691610630258,0.05379381664833003,0.24019999999999975,1.1094897412506723,0.07614543173733954,0.8943654229045972,0.06582028329013485 +16,20,8.399294790580818,0.05897599908052297,13.164133850631297,0.05440876453400187,0.35240000000000116,-4.764839060050478,0.08024015282676315,-4.497381715749114,0.06307518361854694 +16,22,-7.523778213437456,0.05653436802114929,-3.8894414519525182,0.05462046137008848,-0.6546000000000003,-3.634336761484938,0.07860998389410899,-3.661761833816083,0.05869587581824115 +17,22,-15.915381567385271,0.05717156753938731,-11.117321360802961,0.05308899804934327,-0.8948,-4.798060206582311,0.0780194196901893,-4.55612725672068,0.062477292858602894 +19,21,12.079867235940368,0.048820664888398875,9.667020471388009,0.04720065046674738,0.36246000000000045,2.412846764552358,0.0679069858308363,2.511462241396373,0.05869567197629447 diff --git a/summaries/2026_june_08/miscellaneous_set/cdk8/dg_comparison_plot.png b/summaries/2026_june_08/miscellaneous_set/cdk8/dg_comparison_plot.png new file mode 100644 index 0000000..1f38845 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/cdk8/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/cdk8/dg_plot.png b/summaries/2026_june_08/miscellaneous_set/cdk8/dg_plot.png new file mode 100644 index 0000000..6043df3 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/cdk8/dg_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/cdk8/dg_results.csv b/summaries/2026_june_08/miscellaneous_set/cdk8/dg_results.csv new file mode 100644 index 0000000..c7fbec6 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/cdk8/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12,COC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-10.652280538039447,0.03886060817641418,-9.83296 +14,CNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-9.955216897398204,0.031148248115398743,-11.0316 +15,CN(C)C(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.45438457509993,0.043613864642675,-9.72018 +22,CNC(=O)c1cc2c(Oc3ccc(I)cc3)cncc2s1,-11.524906134491363,0.03883496020737251,-11.2901 +13,NC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-12.42324828747824,0.04565082868241195,-11.1972 +19,CC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.891028307009417,0.03853887337437363,-10.2248 +20,CCC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-12.360526016424394,0.04518215449434912,-10.2831 +21,O=C(c1cc2c(Oc3ccc(Cl)cc3)cncc2s1)C1CC1,-9.379566065613044,0.04427117739322905,-9.86234 +17,O=C(NC1CC1)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-6.968778877770683,0.04894137297452357,-10.3953 +16,CCNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-7.86314430067528,0.044011949556480454,-10.6355 diff --git a/summaries/2026_june_08/miscellaneous_set/faah/README.md b/summaries/2026_june_08/miscellaneous_set/faah/README.md new file mode 100644 index 0000000..9fc6268 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/faah/README.md @@ -0,0 +1,40 @@ +# Faah Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.58 +- RMSE: 1.80 +- R²: 0.57 +- Kendall 𝜏: 0.40 +- Spearman ρ: 0.51 + +## System Details +- Ligands: 24 +- Host Atoms: 8446 +- Map Details: + - Edges: 41 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 6.0 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.86 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 4144.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/miscellaneous_set/faah/ddg_results.csv b/summaries/2026_june_08/miscellaneous_set/faah/ddg_results.csv new file mode 100644 index 0000000..1c90a53 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/faah/ddg_results.csv @@ -0,0 +1,42 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +11,12,3.847899084122526,0.0474651964181694,6.840381545969059,0.04858948708034316,1.0765999999999991,-2.9924824618465333,0.06792557048524683,-2.881633378627903,0.07964344609680399 +11,24,10.23390684121516,0.06160740287978773,12.522002586086078,0.06370633528208568,0.49549999999999983,-2.288095744870917,0.08862262264606025,-2.0728119939324294,0.08340359532634506 +11,25,5.469468556072595,0.06326583002798794,5.476849773194383,0.06500947636365464,0.08479999999999954,-0.007381217121787677,0.09071271832663175,-0.430637129298967,0.0764359927796386 +12,27,3.8009282434637623,0.06623022139209539,3.8180454798617,0.06593086202265515,-0.14149999999999885,-0.017117236397937764,0.09345223802936108,-0.09402452191301691,0.08377581847419271 +14,19,-0.28185040075053525,0.05250783495459971,0.5701609298311048,0.05534163577338879,-0.12980000000000036,-0.8520113305816401,0.07628741299646954,-1.5979259219185042,0.06011006472221639 +14,20,9.201646778115423,0.050728585866137474,8.367867619894804,0.051127845866681676,1.0212900000000005,0.8337791582206185,0.07202392690589178,0.9935661786521361,0.055072464583086525 +14,30,0.574594883760505,0.055383155578102715,5.287408836199157,0.057453538388426935,-2.06142,-4.712813952438652,0.07980102126626436,-4.682012306761587,0.05323118644125737 +15,14,5.900804425219713,0.039015218372258534,-0.5449701388854643,0.04137362327044568,0.7477499999999999,6.445774564105177,0.05686795202185308,6.3211006274680415,0.04904090574126832 +19,30,9.371454497415897,0.05391533259525881,11.894469043880077,0.05567758528495165,-1.9316199999999997,-2.523014546464182,0.07750391339810166,-3.084086384843083,0.07006101057037159 +22,28,-4.79760108757063,0.05600074546103446,-2.297390937012082,0.05204442053983949,-1.6167200000000008,-2.500210150558548,0.07645067168782257,-2.8144728591419907,0.06840446670642705 +22,29,2.018465741720146,0.0507836074804358,6.455490880424132,0.053466339072839805,-0.8336199999999998,-4.437025138703986,0.07374024818631174,-3.9910121390313096,0.07385093274746804 +22,31,5.7639187089262185,0.050795378771647234,8.990963374927588,0.05206068185981518,-1.3177200000000013,-3.22704466600137,0.07273572093726713,-3.376525832094333,0.07613401314131579 +23,24,6.8478420571724685,0.05552809310098303,6.54403753243864,0.05648003234821688,-0.9535999999999998,0.30380452473382874,0.0792045653828557,-0.08273033084657477,0.08400441003023448 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2018),10.130181090174355,0.06243115488377109,12.084409675632171,0.061639647709193564,1.8529099999999996,-1.954228585457817,0.08773309107648554,-2.086290636868121,0.07034221880981645 +29,39,3.3891951613550377,0.05452796132585766,4.436333617312307,0.05475632789176482,0.09139999999999837,-1.04713845595727,0.07727583070109754,-0.7351232361511126,0.07818096594392543 +2,14,-1.2879131677094497,0.02726253513250102,-3.012921299239003,0.03198460070362709,0.8226899999999997,1.7250081315295531,0.04202690214637899,1.6762675342324993,0.04734582946800043 +2,15,-6.642478723806909,0.04172727083733814,-1.8265466540529471,0.043416163326236996,0.07493999999999978,-4.815932069753963,0.06021734276355156,-4.644833093235542,0.05575306372950026 +2,20,7.858636663790278,0.05272712068628409,5.075622082917461,0.0547487903098135,1.8439800000000002,2.783014580872816,0.07601038939680481,2.6698337128846354,0.06112585405993991 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3,12,-2.7132775152950135,0.051970947997801456,-0.7984851375458593,0.051780266755392455,-0.4466000000000001,-1.9147923777491545,0.07336331141006235,-1.7672493328222814,0.07221380793595253 +fig 3,14,-2.7739017732365125,0.038689865728949537,-9.724444713181413,0.042523982350798156,2.75708,6.9505429399449,0.05749082348597154,6.921428663740079,0.05326399134346193 +fig 3,23,-2.6378399710150573,0.04252879251669761,-1.8301971603751044,0.04300292514490886,-0.07409999999999961,-0.807642810639953,0.06048098679706664,-0.8756976172802329,0.07324409395775514 diff --git a/summaries/2026_june_08/miscellaneous_set/faah/dg_comparison_plot.png b/summaries/2026_june_08/miscellaneous_set/faah/dg_comparison_plot.png new file mode 100644 index 0000000..27dd7c9 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/faah/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/faah/dg_plot.png b/summaries/2026_june_08/miscellaneous_set/faah/dg_plot.png new file mode 100644 index 0000000..108e2b7 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/faah/dg_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/faah/dg_results.csv b/summaries/2026_june_08/miscellaneous_set/faah/dg_results.csv new file mode 100644 index 0000000..056cd90 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/faah/dg_results.csv @@ -0,0 +1,25 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,CCSc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1,-10.800727380227713,0.05653477053145839,-12.1228 +12,O[C@@H](CNc1cc(-c2ccc(SC(F)(F)F)cc2)ncn1)c1ccccc1,-13.682360758855616,0.05609722120684647,-11.0462 +24,CCOc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1C(F)(F)F,-12.873539374160142,0.061318671172132154,-11.6273 +25,CCOc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1Cl,-11.23136450952668,0.051442013113449474,-12.038 +27,O[C@@H](CNc1cc(-c2ccc(OCC(F)(F)F)c(F)c2)ncn1)c1ccccc1,-13.776385280768633,0.06222129485868181,-11.1877 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3,O[C@@H](CNc1cc(-c2ccc(OC(F)(F)F)cc2)ncn1)c1ccccc1,-11.915111426033334,0.045474562444082677,-10.5996 diff --git a/summaries/2026_june_08/miscellaneous_set/galectin/README.md b/summaries/2026_june_08/miscellaneous_set/galectin/README.md new file mode 100644 index 0000000..248a306 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/galectin/README.md @@ -0,0 +1,40 @@ +# Galectin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.90 +- RMSE: 1.24 +- R²: 0.60 +- Kendall 𝜏: 0.50 +- Spearman ρ: 0.70 + +## System Details +- Ligands: 26 +- Host Atoms: 2712 +- Map Details: + - Edges: 45 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 4.4 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.00 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 4362.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/miscellaneous_set/galectin/ddg_results.csv b/summaries/2026_june_08/miscellaneous_set/galectin/ddg_results.csv new file mode 100644 index 0000000..660dd39 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/galectin/ddg_results.csv @@ -0,0 +1,46 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) 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-0.09 +- Spearman ρ: -0.12 + +## System Details +- Ligands: 13 +- Host Atoms: 3626 +- Map Details: + - Edges: 22 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 7.5 + - Median Dummy Atoms: 7.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.52 Hours +- Average Time Per Edge: 0.11 Hours +- Total Nanoseconds Simulated: 2564.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/miscellaneous_set/hiv1_protease/ddg_results.csv 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a/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_comparison_plot.png b/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_comparison_plot.png new file mode 100644 index 0000000..f59e531 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_plot.png b/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_plot.png new file mode 100644 index 0000000..01b44bf Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_results.csv b/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_results.csv new file mode 100644 index 0000000..2ed0aab --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/hiv1_protease/dg_results.csv @@ -0,0 +1,14 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccccn2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-9.939019844163706,0.049046851808971025,-10.806 +11 (2cen),COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2cccnc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.683824316044351,0.04995688717184046,-11.3247 +17,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2c(C)noc2C)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.539863908858054,0.055688011581247164,-11.4873 +18,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2cnccn2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.076930470768076,0.05297469303717227,-11.8386 +12,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccncc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-9.61070392972621,0.054960935297570304,-11.2682 +19,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccc3c(c2)OCO3)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-11.22704995758955,0.04913534748214916,-10.8575 +13,COC(=O)N[C@H](C(=O)NN(Cc1ccc(/C=C/c2ccccc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.421600483159402,0.0547916199563337,-10.8575 +20,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2cc3ccccc3s2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.127156557303621,0.05657478251397415,-11.536 +14,COC(=O)N[C@H](C(=O)NN(Cc1ccc(C#Cc2ccccc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-13.800535097688693,0.05714062406923332,-10.6737 +15,COC(=O)N[C@H](C(=O)NN(Cc1ccc(C#Cc2ccccn2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-13.556612170077287,0.056656516837719724,-10.9764 +16,COC(=O)N[C@H](C(=O)NN(Cc1ccc(C#Cc2cccnc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-13.837214079517135,0.05947208324105937,-11.0612 +1,COC(=O)N[C@H](C(=O)NN(Cc1ccc(Br)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-11.040653675566793,0.0394801345475223,-11.7595 +9,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccccc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.08873550953712,0.05233593576504981,-10.5033 diff --git a/summaries/2026_june_08/miscellaneous_set/malt1/README.md b/summaries/2026_june_08/miscellaneous_set/malt1/README.md new file mode 100644 index 0000000..2f02168 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/malt1/README.md @@ -0,0 +1,40 @@ +# Malt1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.58 +- RMSE: 1.78 +- R²: 0.52 +- Kendall 𝜏: 0.47 +- Spearman ρ: 0.59 + +## System Details +- Ligands: 16 +- Host Atoms: 6224 +- Map Details: + - Edges: 26 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 14 + - Mean Dummy Atoms: 8.5 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.90 Hours +- Average Time Per Edge: 0.11 Hours +- Total Nanoseconds Simulated: 2767.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/miscellaneous_set/malt1/ddg_results.csv b/summaries/2026_june_08/miscellaneous_set/malt1/ddg_results.csv new file mode 100644 index 0000000..cf8a052 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/malt1/ddg_results.csv @@ -0,0 +1,27 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) 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+Pfizer-01-09,Pfizer-01-06,20.89155108991294,0.07248835264133487,19.441142010914444,0.07140578886196058,,1.4504090789984998,0.10175140270115893,1.6698297758004577,0.06936071065229533 +Pfizer-01-12,Pfizer-01-07,4.74298887197223,0.059570909951663996,7.42133780501345,0.059912857435393235,,-2.678348933041221,0.08448812815149248,-2.562401453360538,0.08295177272510912 +Pfizer-01-12,Pfizer-01-11,-18.772614690193326,0.053082967717792064,-26.32864900721852,0.056477574355238036,,7.556034317025194,0.07750817935405009,8.38235773011257,0.08178875920756917 +Pfizer-01-13,Pfizer-01-04,-4.855986213201123,0.05435714258964661,-4.0296143059492,0.054128985475387636,,-0.8263719072519234,0.07671144646730303,-1.8889488362356541,0.06596496554003639 +Pfizer-01-13,Pfizer-01-05,-4.320200189598847,0.04395061807048613,-3.2854583835628715,0.045710576302697384,,-1.0347418060359748,0.06341225129817157,-0.927071156155387,0.06850713963481013 +Pfizer-01-13,Pfizer-01-12,18.145190157183446,0.05391337001900939,22.23085261041231,0.057316507806914066,,-4.0856624532288635,0.07868820454163801,-3.133411943351396,0.07753106161543125 diff --git a/summaries/2026_june_08/miscellaneous_set/malt1/dg_comparison_plot.png b/summaries/2026_june_08/miscellaneous_set/malt1/dg_comparison_plot.png new file mode 100644 index 0000000..d8702f1 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/malt1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/malt1/dg_plot.png b/summaries/2026_june_08/miscellaneous_set/malt1/dg_plot.png new file mode 100644 index 0000000..832f460 Binary files /dev/null and b/summaries/2026_june_08/miscellaneous_set/malt1/dg_plot.png differ diff --git a/summaries/2026_june_08/miscellaneous_set/malt1/dg_results.csv b/summaries/2026_june_08/miscellaneous_set/malt1/dg_results.csv new file mode 100644 index 0000000..b0d1046 --- /dev/null +++ b/summaries/2026_june_08/miscellaneous_set/malt1/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1832576-04-1,CO[C@@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.970754851806293,0.04749821295543992,-10.031196069300446 +1832577-09-9,CO[C@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.319778667424195,0.04302709040564021,-8.385343719764283 +2714550-01-1,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-11.047977423138558,0.04694869701162288,-8.771566645289406 +Pfizer-01-01,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2ccnn12,-8.384503105359254,0.04505213644616854,-8.845471319203405 +Pfizer-01-02,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-8.659203560108566,0.048734830684031165,-8.584573845890262 +Pfizer-01-07,Cn1ncc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)c21,-9.139261522835405,0.058592010926270484,-6.463477018541003 +Pfizer-01-03,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)n2n1,-7.125173173879664,0.04618135068386157,-8.323545811509687 +Pfizer-01-06,Cc1nc2c(C3CC3)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1C,-4.552218803471148,0.05413407273420425,-6.6378646965251065 +Pfizer-01-04,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,-5.332396962359125,0.042288107280136704,-7.187253218618596 +Pfizer-01-05,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)cn2n1,-4.370519282278858,0.04615339120348076,-6.671495008018873 +Pfizer-01-08,CCOc1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(C)nn12,-7.277180813103289,0.057084413284185544, +Pfizer-01-10,Cc1nc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-7.493836068176302,0.04859751182417513, +Pfizer-01-11,Cc1cc2nnc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,1.8054976606377036,0.056933542651584346, +Pfizer-01-09,Cc1cn2c(C(C)C)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1,-6.222048579271606,0.043363698543820266, +Pfizer-01-12,Cc1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)ccc2cncn12,-6.576860069474867,0.05871944187280698, +Pfizer-01-13,O=C(Nc1ccnc(C(F)(F)F)c1)Nc1cnc2ccnn2c1,-3.443448126123471,0.050626995381533736, diff --git a/summaries/2026_june_08/scaffold_hopping_set/bace1/README.md b/summaries/2026_june_08/scaffold_hopping_set/bace1/README.md new file mode 100644 index 0000000..808dd2d --- /dev/null +++ b/summaries/2026_june_08/scaffold_hopping_set/bace1/README.md @@ -0,0 +1,40 @@ +# Bace1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.77 +- RMSE: 1.92 +- R²: 0.71 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 6106 +- Map Details: + - Edges: 3 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 6.7 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.47 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 383.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/scaffold_hopping_set/bace1/ddg_results.csv b/summaries/2026_june_08/scaffold_hopping_set/bace1/ddg_results.csv new file mode 100644 index 0000000..0671b54 --- /dev/null +++ b/summaries/2026_june_08/scaffold_hopping_set/bace1/ddg_results.csv @@ -0,0 +1,4 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +31,6,-12.679018556734652,0.03753172847169786,-14.347034605116598,0.038302414904477396,0.5200000000000005,1.6680160483819446,0.05362560609995927,1.5503018684956995,0.04703693635489975 +31,7,8.388056999916701,0.07058137634802772,3.658383754971223,0.06992968795880067,0.6399999999999997,4.729673244945477,0.09935739502018538,5.133769426394268,0.05659128480483612 +7,6,-21.833263993582502,0.068763039589547,-17.869382861663343,0.06756464054034189,-0.11999999999999922,-3.9638811319191563,0.09640195156188083,-3.583467557898569,0.057244128977979696 diff --git a/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_comparison_plot.png b/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_comparison_plot.png new file mode 100644 index 0000000..a15bc0a Binary files /dev/null and b/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_plot.png b/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_plot.png new file mode 100644 index 0000000..94c5a87 Binary files /dev/null and b/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_plot.png differ diff --git a/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_results.csv b/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_results.csv new file mode 100644 index 0000000..56086af --- /dev/null +++ b/summaries/2026_june_08/scaffold_hopping_set/bace1/dg_results.csv @@ -0,0 +1,4 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +31,NC1=[NH+][C@@H]2CC[C@H](OC(=O)c3cccc(Cl)c3)C[C@@H]2CS1,-10.191357098296656,0.03269676279900956,-8.35 +6,NC1=[NH+][C@@H]2CC[C@H](NC(=O)c3cccc(Cl)c3)C[C@@H]2CS1,-8.641055229800957,0.03381412551168808,-7.829999999999999 +7,NC1=[NH+][C@]23CC[C@H](NC(=O)c4cccc(Cl)c4)C[C@@H]2[C@@H](COC3)S1,-5.057587671902388,0.04618977395839235,-7.71 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/2EP9/README.md b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/README.md new file mode 100644 index 0000000..e38ae29 --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/README.md @@ -0,0 +1,40 @@ +# 2Ep9 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.92 +- RMSE: 1.11 +- R²: 0.06 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.80 + +## System Details +- Ligands: 4 +- Host Atoms: 4374 +- Map Details: + - Edges: 6 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 14 + - Mean Dummy Atoms: 10.2 + - Median Dummy Atoms: 11.5 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.95 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 1022.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/2EP9/ddg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/ddg_results.csv new file mode 100644 index 0000000..fc6d3ee --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/ddg_results.csv @@ -0,0 +1,7 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +ligand_4,ligand_6,17.13629667076438,0.051199332408248865,19.390923072813216,0.05063270061882577,-0.20999999999999908,-2.254626402048833,0.07200723582395038,-2.1744349285814657,0.05491946001456281 +ligand_5,ligand_4,-0.8370768705203327,0.08265014450347245,-4.368172564307676,0.08257733190916446,0.29999999999999893,3.531095693787343,0.11683348035422546,3.1361601830933203,0.060430874776800515 +ligand_5,ligand_6,15.991451432574172,0.07530899237918448,15.025029977758127,0.07434137705160368,0.08999999999999986,0.9664214548160444,0.1058210029960819,0.9617252545118546,0.05648678430064292 +ligand_5,ligand_7,17.89566349908275,0.08083925946134744,17.116181020891187,0.08224174495891225,0.9100000000000001,0.7794824781915664,0.1153199483356883,1.1698289400922786,0.06071634579431664 +ligand_7,ligand_4,-20.448191054964184,0.07987900661614492,-21.85696503832804,0.07859567504826263,-0.6100000000000012,1.4087739833638568,0.1120621962763278,1.9663312430010418,0.05926098998733345 +ligand_7,ligand_6,-3.0264269666414014,0.07514896889645667,-2.983647257721261,0.07307621294369818,-0.8200000000000003,-0.04277970892014047,0.1048212784905495,-0.2081036855804239,0.05523342383572514 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/2EP9/dg_plot.png b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/dg_plot.png new file mode 100644 index 0000000..ccfccfa Binary files /dev/null and b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/dg_plot.png differ diff --git a/summaries/2026_june_08/schrodinger_macrocycles/2EP9/dg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/dg_results.csv new file mode 100644 index 0000000..fcebc58 --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/2EP9/dg_results.csv @@ -0,0 +1,5 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +ligand_4,O=C1Nc2cncc(n2)OCCCCCOc2ccc(Cl)cc2N1,-9.035768411331043,0.041697007770061564,-10.88 +ligand_6,N#Cc1ncc2nc1OCCCCCOc1ccc(Cl)cc1NC(=O)N2,-11.210203339912509,0.03574222476727755,-11.09 +ligand_5,N#Cc1ncc2nc1OCCCCOc1ccc(Cl)cc1NC(=O)N2,-12.171928594424363,0.04374071523549621,-11.18 +ligand_7,N#Cc1ncc2nc1OCCCCCCOc1ccc(Cl)cc1NC(=O)N2,-11.002099654332085,0.042109672016085106,-10.27 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/README.md b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/README.md new file mode 100644 index 0000000..c812993 --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/README.md @@ -0,0 +1,40 @@ +# 3Rkz Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.31 +- RMSE: 1.40 +- R²: 0.60 +- Kendall 𝜏: 0.62 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 7 +- Host Atoms: 3289 +- Map Details: + - Edges: 12 + - Min Dummy Atoms: 8 + - Max Dummy Atoms: 39 + - Mean Dummy Atoms: 26.2 + - Median Dummy Atoms: 28.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.35 Hours +- Average Time Per Edge: 0.20 Hours +- Total Nanoseconds Simulated: 2549.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/ddg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/ddg_results.csv new file mode 100644 index 0000000..a136fab --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/ddg_results.csv @@ -0,0 +1,13 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +ligand_62,lignad_65,18.92702236212061,0.08604895673172765,22.150862509982574,0.08618326563456216,-2.6099999999999994,-3.2238401478619636,0.12178660940372814,-3.340211562420767,0.07405687518426719 +ligand_62,ligand_64,10.595418537642397,0.08723872488506851,13.13581170297494,0.08737121844701026,-2.2200000000000006,-2.5403931653325444,0.1234679105374666,-1.9404328359597303,0.08799288330805481 +ligand_62,lignad_68,24.16459090893244,0.0866145661546177,24.747604851822523,0.08611829486331496,-1.7799999999999994,-0.5830139428900808,0.12214108146040588,-1.053098972015177,0.07719071766951013 +ligand_69,ligand_70,-43.4334904019927,0.0680270885661998,-44.160214315356036,0.0672145338128971,0.40000000000000036,0.7267239133633401,0.09563199430357332,0.7815252496256981,0.09324357861755218 +ligand_69,lignad_65,7.494866184662726,0.09141092006098898,7.088204196513693,0.09103398778156922,3.860000000000001,0.4066619881490335,0.12900830685584327,0.3764857254926568,0.07893848541739448 +lignad_63,ligand_64,7.841732202834878,0.09144154437880149,9.330974251193103,0.08796261507102553,0.4299999999999997,-1.4892420483582252,0.12688174686893985,-1.6461373979149094,0.08937013664483659 +lignad_63,ligand_69,-0.5180125918560462,0.10524349578467512,3.000488890222526,0.10917605844442214,-3.8200000000000003,-3.5185014820785723,0.15164301877250666,-3.422401849868603,0.08886645061671893 +lignad_63,ligand_70,-28.812762658258354,0.10751656376498442,-26.440257294804926,0.10474981129554291,-3.42,-2.372505363453427,0.15010774280589864,-2.6408766002429047,0.09050842527922676 +lignad_63,lignad_68,29.20077527427386,0.07338831437794734,30.15079593229036,0.07453288704838544,0.870000000000001,-0.9500206580165003,0.10459921576667683,-0.7588035339703563,0.07875709939672634 +lignad_65,ligand_64,-4.024389727223447,0.08851195111327859,-5.898710273668309,0.09050798095632909,0.3899999999999988,1.8743205464448613,0.12659407611207818,1.3997787264610366,0.07950509265886822 +lignad_65,ligand_70,-36.50643836770835,0.09136644016746538,-36.815672989065874,0.0885439967570268,-3.460000000000001,0.3092346213575256,0.1272315438505067,0.40503952413304134,0.08078250727294758 +lignad_65,lignad_68,19.01129269712585,0.06956481064409142,16.863346387451095,0.07125774149422846,0.8300000000000001,2.1479463096747535,0.09958377680529387,2.28711259040559,0.06735517159182576 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/dg_plot.png b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/dg_plot.png new file mode 100644 index 0000000..04d583e Binary files /dev/null and b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/dg_plot.png differ diff --git a/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/dg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/dg_results.csv new file mode 100644 index 0000000..321e44e --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/3RKZ/dg_results.csv @@ -0,0 +1,8 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +ligand_62,Cc1c2c(n3c1CC[NH2+]CCNc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-7.88715598076548,0.05876269444225588,-6.67 +lignad_65,Cc1c2c(n3c1CCC[N@@H+](C)C[C@H](C)Nc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-11.227367543186247,0.04507068341998155,-9.28 +ligand_64,Cc1c2c(n3c1CCC[NH2+]CC(C)(C)CNc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-9.82758881672521,0.06549574989837907,-8.89 +lignad_68,Cc1c2c(n3c1CCC[N@H+]1CCC[C@@H]1CNc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-8.940254952780657,0.05005349774211681,-8.45 +ligand_69,Cc1c2c(n3c1CCN(C(=O)[C@@H]1CCC[NH2+]1)C[C@@H](C)[C@H](C)Nc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-11.603853268678904,0.06480677415246035,-13.14 +ligand_70,Cc1c2c(n3c1CCN(C(=O)[C@H](C)[NH3+])C[C@@H](C)[C@H](C)Nc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-10.822328019053206,0.067040636761293,-12.74 +lignad_63,Cc1c2c(n3c1CCC[NH2+]C(C)(C)CNc1cc-3ccc1C(N)=O)CC(C)(C)CC2=O,-8.181451418810301,0.06080565820025091,-9.32 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/MHT1/README.md b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/README.md new file mode 100644 index 0000000..85a3353 --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/README.md @@ -0,0 +1,40 @@ +# Mht1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.06 +- RMSE: 1.18 +- R²: 0.87 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 2487 +- Map Details: + - Edges: 3 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 19 + - Mean Dummy Atoms: 12.7 + - Median Dummy Atoms: 14.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.36 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 405.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/MHT1/ddg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/ddg_results.csv new file mode 100644 index 0000000..2a600de --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/ddg_results.csv @@ -0,0 +1,4 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +5AN26_ligand,5ANT_A_ligand,10.51207248859785,0.046089731529584586,14.472444133504078,0.05031882283203717,-0.9800000000000004,-3.960371644906228,0.06823670041606003,-3.7982656240070893,0.05263867113098616 +5AN26_ligand,5ANU_ligand,18.510402747917322,0.07719297081700467,25.435528197703743,0.07481727722998613,-5.390000000000001,-6.92512544978642,0.10750060332697457,-7.327457761104026,0.056379746076053935 +5ANT_A_ligand,5ANU_ligand,6.777817191652643,0.070135790885482,10.65014826156378,0.07026458121724306,-4.41,-3.8723310699111386,0.09927809696386514,-3.5291921370969366,0.05758311539022857 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/MHT1/dg_plot.png b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/dg_plot.png new file mode 100644 index 0000000..43aacc2 Binary files /dev/null and b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/dg_plot.png differ diff --git a/summaries/2026_june_08/schrodinger_macrocycles/MHT1/dg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/dg_results.csv new file mode 100644 index 0000000..f087a38 --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/MHT1/dg_results.csv @@ -0,0 +1,4 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +5AN26_ligand,COCCOc1nc(N)c2[nH]c(=O)n(Cc3ccccc3)c2n1,-5.984758871629629,0.03628836099903147,-7.57 +5ANT_A_ligand,CNc1nc(OCCOC)nc2c1[nH]c(=O)n2Cc1ccccc1,-9.783024495636718,0.03813114939836049,-8.55 +5ANU_ligand,CNc1nc2nc3c1[nH]c(=O)n3Cc1cccc(c1)OCCOCCO2,-13.312216632733655,0.04314893537046182,-12.96 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/hsp90/README.md b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/README.md new file mode 100644 index 0000000..e2bf5fe --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/README.md @@ -0,0 +1,40 @@ +# Hsp90 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.83 +- RMSE: 1.01 +- R²: 0.70 +- Kendall 𝜏: 0.56 +- Spearman ρ: 0.73 + +## System Details +- Ligands: 10 +- Host Atoms: 3366 +- Map Details: + - Edges: 17 + - Min Dummy Atoms: 7 + - Max Dummy Atoms: 31 + - Mean Dummy Atoms: 19.2 + - Median Dummy Atoms: 21.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.70 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 3212.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/hsp90/ddg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/ddg_results.csv new file mode 100644 index 0000000..926d495 --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/ddg_results.csv @@ -0,0 +1,18 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +13,"11, 3VHC",-10.201675627521,0.08031914136535603,-8.463116263995731,0.0791489166953195,-0.9310999999999989,-1.7385593635252692,0.11276398132254233,-1.2794496188994415,0.0861554425968318 +"11, 3VHC","17, top conformer",-38.01172860432039,0.08922383708072672,-37.99339928534247,0.08848976323825118,-0.7330000000000005,-0.018329318977919663,0.12566356393708486,0.9477188960132583,0.08900071455207924 +13,12,-5.051133811474786,0.07479875268709564,-5.50612892462231,0.07428822552896608,0.1053999999999995,0.45499511314752383,0.10542103137319339,-0.014201815208791047,0.09399509559449408 +13,9,7.6622609562982325,0.08272257945155022,5.157734212355549,0.08288954097097524,1.5533000000000001,2.5045267439426837,0.11710551290821888,2.5883530456314823,0.0871708808402899 +"16, 3VHD",12,39.19764202945502,0.09021163034009472,37.14230321398012,0.09137813243881986,1.5825999999999993,2.0553388154748973,0.12840600194938087,2.0731802186444135,0.079443640790609 +"16, 3VHD","17, top conformer",1.8758483009854656,0.07581127512641514,-0.34789694538465865,0.07329089483348408,-0.18689999999999962,2.2237452463701244,0.10544621710514719,1.7556513109670213,0.08756806715592674 +"16, 3VHD",7,41.91239276839805,0.0902153804076253,40.14147219046907,0.08747206347610843,3.243080000000001,1.7709205779289858,0.12565897003740276,2.3654307797288503,0.0860597050371088 +18 minimized,"11, 3VHC",24.88765556553615,0.09043961872016097,26.75107463437946,0.08843159554656829,0.9826000000000015,-1.8634190688433077,0.12648901819984185,-1.5446755355153474,0.08736974814690705 +18 minimized,"16, 3VHD",-1.5330073448978268,0.0765007619143506,0.8101055661483422,0.07336036879316002,0.43650000000000055,-2.343112911046169,0.10599108586548493,-2.3526079504691104,0.08590990679716848 +18 minimized,"17, top conformer",-0.8857214341543643,0.07671551925300299,-0.5048652290370531,0.07377377286375968,0.24960000000000093,-0.3808562051173112,0.10643232806253689,-0.5969566395020891,0.10199345528696267 +"8, 3VHA","11, 3VHC",-13.330262322640994,0.061179525920278456,-10.512913285081444,0.0602868312129667,-2.0421999999999993,-2.817349037559551,0.08589200433993119,-2.779369753116921,0.07335293731488073 +"8, 3VHA",9,4.491201115028657,0.07408921078015548,3.4340560556545756,0.07174107078252642,0.4421999999999997,1.0571450593740817,0.10313094778508425,1.088432911414003,0.0745429781410487 +9,12,-14.566673769360303,0.059682862944096575,-11.661537037724285,0.06159191734349971,-1.4479000000000006,-2.905136731636017,0.08576484367881934,-2.6025548608402733,0.08209905629688535 +9,7,-9.1868946218027,0.07864673345611854,-7.290910687166448,0.08203134138801478,0.21258000000000088,-1.895983934636251,0.11364176016427581,-2.3103042997558365,0.08851686739738368 +lig_3B27,"16, 3VHD",33.91790421224051,0.08212314700368256,39.78515638679768,0.08182783018784975,-5.7008,-5.8672521745571755,0.11593103582319979,-5.901134614967029,0.08169874027991755 +lig_3B27,7,65.17433079432318,0.07727967608803542,68.64510866073671,0.07541160714968395,-2.4577199999999992,-3.4707778664135276,0.10797712178591322,-3.535703835238179,0.09713363703913375 +lig_3B27,"8, 3VHA",68.46694726758068,0.08081901935271897,70.88326547281743,0.07833845802331477,-3.1125,-2.416318205236745,0.11255499942075348,-2.3138324468963454,0.08459529077165603 diff --git a/summaries/2026_june_08/schrodinger_macrocycles/hsp90/dg_plot.png b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/dg_plot.png new file mode 100644 index 0000000..9bbcca8 Binary files /dev/null and b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/dg_plot.png differ diff --git a/summaries/2026_june_08/schrodinger_macrocycles/hsp90/dg_results.csv b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/dg_results.csv new file mode 100644 index 0000000..7dfccff --- /dev/null +++ b/summaries/2026_june_08/schrodinger_macrocycles/hsp90/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +13,Cc1cc(C)c2cc1C(=O)NCCCCCOc1cccc(c1)Sc1cc-2nc(N)n1,-11.459535623260674,0.06961891056836121,-11.2636 +"11, 3VHC",Cc1cc(C)c2cc1C(=O)NCCCOc1cccc(c1)Sc1cc-2nc(N)n1,-12.738985242160116,0.05075399078230699,-12.1947 +"17, top conformer",Cc1cc(C)c2cc1C(=O)NCCCCNC(=O)CCSc1cc-2nc(N)n1,-11.791266346146857,0.07311059848236907,-12.9277 +12,Cc1cc(C)c2cc1C(=O)NCCCCOc1cccc(c1)Sc1cc-2nc(N)n1,-11.473737438469465,0.0631528723582119,-11.1582 +9,Cc1ccc2cc1-c1cc(nc(N)n1)Sc1cccc(c1)OCCCCCO2,-8.871182577629192,0.05245921994984814,-9.7103 +"16, 3VHD",Cc1cc(C)c2cc1C(=O)NCCCNC(=O)CCSc1cc-2nc(N)n1,-13.546917657113879,0.04819758059254333,-12.7408 +7,Cc1ccc2cc1-c1cc(nc(N)n1)Sc1cccc(c1)OCCCO2,-11.181486877385028,0.07129702697938717,-9.49772 +18 minimized,Cc1cc(C)c2cc1C(=O)NCCCCCNC(=O)CCSc1cc-2nc(N)n1,-11.194309706644768,0.07111613959519643,-13.1773 +"8, 3VHA",Cc1ccc2cc1-c1cc(nc(N)n1)Sc1cccc(c1)OCCCCO2,-9.959615489043195,0.05295928466652773,-10.1525 +lig_3B27,CSc1nc(N)nc(-c2ccccc2Cl)n1,-7.645783042146849,0.06596724481400382,-7.04 diff --git a/summaries/2026_june_08/water_set/brd4/README.md b/summaries/2026_june_08/water_set/brd4/README.md new file mode 100644 index 0000000..98ac6bd --- /dev/null +++ b/summaries/2026_june_08/water_set/brd4/README.md @@ -0,0 +1,40 @@ +# Brd4 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.35 +- RMSE: 1.69 +- R²: 0.02 +- Kendall 𝜏: 0.14 +- Spearman ρ: -0.02 + +## System Details +- Ligands: 8 +- Host Atoms: 2499 +- Map Details: + - Edges: 13 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.92 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 1124.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/brd4/ddg_results.csv b/summaries/2026_june_08/water_set/brd4/ddg_results.csv new file mode 100644 index 0000000..2185314 --- /dev/null +++ b/summaries/2026_june_08/water_set/brd4/ddg_results.csv @@ -0,0 +1,14 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +cmpd 2 (methyl),cmpd 6 (ethyl),3.9313213564969827,0.04551244722169674,4.053507591893307,0.04365350419414572,1.0,-0.12218623539632396,0.0630635495396194,-0.015649302785475605,0.05346425746948136 +cmpd 2 (methyl),cmpd 3 (Allyl),4.72251261182116,0.05506116464948897,5.464993161548285,0.05206204084927104,2.5,-0.7424805497271251,0.07577722580003375,-0.8439036206868238,0.0524074430869636 +cmpd 3 (Allyl),cmpd 4 (Crotyl),1.6448099849274658,0.04088473198169503,5.23791083324924,0.04055866363690253,-1.5500000000000007,-3.5931008483217743,0.05758963887042908,-3.000963059440851,0.05021728763403776 +cmpd 2 (methyl),cmpd 7 (n-propyl),5.804291992347427,0.05162646746944496,6.579507755091705,0.05132007305479224,2.5700000000000003,-0.7752157627442777,0.0727945193110228,-0.8235716288833315,0.0553798215375088 +cmpd 3 (Allyl),cmpd 6 (ethyl),1.908263169491243,0.049880147876181224,0.4623356130500849,0.0488854828715902,-1.5,1.4459275564411582,0.06984138878729607,0.8282543179013482,0.049519569866709925 +cmpd 3 (Allyl),cmpd 8 (n-Butyl),11.103889759981735,0.05778277118335902,13.074273898777784,0.05653556717352158,-0.5700000000000012,-1.9703841387960492,0.08084008288751439,-2.425053455672211,0.050037359630784706 +cmpd 5 (1-Butenyl),cmpd 7 (n-propyl),0.07369606626428536,0.04577472778088653,-0.8473520273771421,0.04767838239816175,0.6200000000000001,0.9210480936414275,0.06609503651197725,1.397072682115156,0.05762102366003947 +cmpd 5 (1-Butenyl),cmpd 8 (n-Butyl),7.976304902052955,0.052281731971516504,8.752836634441023,0.05315544953835474,-0.02000000000000135,-0.7765317323880677,0.07455790577508242,-1.0483127653605475,0.0562426361393562 +cmpd 5 (1-Butenyl),cmpd 9 (methoxyethyl),-5.96896902928307,0.04911574001738294,-7.129470775148116,0.049271236873935975,0.41999999999999993,1.160501745865046,0.06957018542840503,0.8697388109226285,0.05825972863433616 +cmpd 6 (ethyl),cmpd 7 (n-propyl),2.484960374306606,0.044801391004313657,2.9170305381188224,0.04192077147341388,1.5700000000000003,-0.4320701638122162,0.06135564942894491,-0.8079223260978559,0.052655221416275134 +cmpd 8 (n-Butyl),cmpd 4 (Crotyl),-9.074652001882988,0.053256431955206476,-8.959394085708581,0.05237148271784919,-0.9799999999999995,-0.11525791617440764,0.07469283597953363,-0.5759096037686398,0.05181903387951056 +cmpd 9 (methoxyethyl),cmpd 4 (Crotyl),5.055490289534111,0.05011779299664735,7.042020221136534,0.052683543102259034,-1.4200000000000008,-1.986529931602422,0.07271415879085984,-2.4939611800518158,0.05400161231711823 +cmpd 9 (methoxyethyl),cmpd 8 (n-Butyl),12.165151058605312,0.04089089855776094,14.202165255035771,0.04052194596024354,-0.4400000000000013,-2.037014196430459,0.057568165588856426,-1.918051576283176,0.05383433397330311 diff --git a/summaries/2026_june_08/water_set/brd4/dg_comparison_plot.png b/summaries/2026_june_08/water_set/brd4/dg_comparison_plot.png new file mode 100644 index 0000000..d79134c Binary files /dev/null and b/summaries/2026_june_08/water_set/brd4/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/water_set/brd4/dg_plot.png b/summaries/2026_june_08/water_set/brd4/dg_plot.png new file mode 100644 index 0000000..75b3a26 Binary files /dev/null and b/summaries/2026_june_08/water_set/brd4/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/brd4/dg_results.csv b/summaries/2026_june_08/water_set/brd4/dg_results.csv new file mode 100644 index 0000000..de7a7ea --- /dev/null +++ b/summaries/2026_june_08/water_set/brd4/dg_results.csv @@ -0,0 +1,9 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 2 (methyl),CN(C)C(=O)c1cccc(-c2cn(C)c(=O)c3[nH]ccc23)c1,-6.385187735010414,0.03970377260344637,-9.59 +cmpd 6 (ethyl),CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-6.400837037795889,0.03580554800330271,-8.59 +cmpd 3 (Allyl),C=CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.229091355697237,0.034207463103351446,-7.09 +cmpd 4 (Crotyl),C/C=C/Cn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-10.230054415138088,0.03676445899714194,-8.64 +cmpd 7 (n-propyl),CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.208759363893745,0.03860744843395047,-7.02 +cmpd 8 (n-Butyl),CCCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.654144811369449,0.03651830810502223,-7.660000000000001 +cmpd 5 (1-Butenyl),C=CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.605832046008901,0.04277437659453009,-7.64 +cmpd 9 (methoxyethyl),COCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.736093235086273,0.03955437633809696,-7.22 diff --git a/summaries/2026_june_08/water_set/chk1/README.md b/summaries/2026_june_08/water_set/chk1/README.md new file mode 100644 index 0000000..3ec4c59 --- /dev/null +++ b/summaries/2026_june_08/water_set/chk1/README.md @@ -0,0 +1,40 @@ +# Chk1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 2.29 +- RMSE: 2.97 +- R²: 0.03 +- Kendall 𝜏: -0.43 +- Spearman ρ: -0.45 + +## System Details +- Ligands: 13 +- Host Atoms: 4834 +- Map Details: + - Edges: 22 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 5.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.52 Hours +- Average Time Per Edge: 0.11 Hours +- Total Nanoseconds Simulated: 2579.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/chk1/ddg_results.csv b/summaries/2026_june_08/water_set/chk1/ddg_results.csv new file mode 100644 index 0000000..d2c150b --- /dev/null +++ b/summaries/2026_june_08/water_set/chk1/ddg_results.csv @@ -0,0 +1,23 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +13 docked,12 docked,0.21331479760674293,0.049592381359356404,0.19184905075463082,0.04721219039709769,1.30842,0.021465746852112118,0.06847185707269551,-0.30548354949236156,0.06711157473814974 +12 docked,11 docked,6.152709185694906,0.058150885345226354,2.933522683871956,0.0577289832242504,-2.36627,3.21918650182295,0.08193998395496209,2.61772618995578,0.07347719822146961 +14 docked,11 docked,9.238015244811281,0.05804871088435633,10.433747983730564,0.056792621461828126,-0.10859999999999914,-1.1957327389192816,0.08120994205047859,-0.5793895593305187,0.0700879230304907 +14 docked,12 docked,4.110103560814973,0.06502457833984827,7.140110769995371,0.06474946961350783,2.257670000000001,-3.0300072091803987,0.09176431552355,-3.197115749286299,0.06461479187883452 +14 docked,13 docked,4.871635236996483,0.06180666362071643,7.065816407126678,0.06221027604963632,0.949250000000001,-2.194181170130195,0.08769368343328011,-2.8916321997939374,0.06338281912383757 +16 docked,17 torsion adjust,7.4619600472727825,0.04345411589545257,7.552483113262108,0.043998435618624536,1.457699999999999,-0.09052306598932564,0.061839490013596274,-0.4608539981970452,0.06005442815584432 +16 docked,19,-2.3427696794169734,0.03857654581794982,-2.2025062512237743,0.040264413722485556,1.5321999999999996,-0.14026342819319923,0.05576175122483031,0.10464725563807242,0.05545770976420114 +17 torsion adjust,15 docked,-8.508557280344057,0.06002902702773459,-8.639950228722547,0.05843447734887804,0.2801000000000009,0.13139294837849075,0.0837739352599186,0.03178811027014028,0.06935904250977949 +18 docked,13 docked,-1.4204672561738068,0.056986489728241135,-1.1742490888397055,0.05547418680641149,-0.3712699999999991,-0.24621816733410118,0.07952889671924018,-0.11366313470322709,0.06188623415117245 +18 docked,19,-10.862694049441224,0.036575625210963025,-12.079085869980158,0.03663216008446614,-0.699819999999999,1.2163918205389341,0.05176573685389583,1.2267966369615522,0.0587174103646348 +18 docked,15 docked,-9.89825694792517,0.05435247651698359,-10.738856492442041,0.054628722743838225,-0.49421999999999855,0.8405995445168726,0.07706159258769832,0.6930834933965748,0.0643855868153937 +19,17 torsion adjust,8.8846322486978,0.047789225750383135,9.833909765054777,0.04857659305111936,-0.07450000000000045,-0.9492775163569775,0.06814319841536014,-0.5655012538351176,0.06413195200709021 +20,11 docked,-2.769066829453367,0.06976603243353494,-4.8268930446193,0.06834138058025742,-0.8963999999999999,2.0578262151659334,0.09766188397288184,2.020871881348139,0.07363959064229623 +20,15 docked,-17.215843048596366,0.05992427827399197,-17.446297003265588,0.060897782607647215,0.03850000000000087,0.23045395466922153,0.08543687174274985,0.5153758689845223,0.06959491308616558 +21 (Xtal),14 docked,0.6765284924173836,0.06381222793028232,0.018941958943841118,0.06267665129231034,2.1984999999999992,0.6575865334735425,0.0894447485917657,0.2764906682795001,0.06745047565744791 +21 (Xtal),16 docked,-3.18734545984081,0.054355308922399634,-1.6603856177704155,0.052816722320908255,1.2870000000000008,-1.5269598420703945,0.07578987903917928,-1.3793290154877305,0.06316576743859013 +21 (Xtal),22,-2.4132571436355357,0.047762746278277236,-2.2418214047712897,0.04620182513280956,0.0,-0.1714357388642464,0.06645215254335858,-0.07457963013993307,0.07153957724146183 +22,14 docked,2.4852783770879032,0.06917144077061328,2.3051365789145084,0.06855138394256818,2.1984999999999992,0.18014179817339493,0.09738573026231233,0.35107029841943316,0.06524441793185885 +22,16 docked,-1.0420150531955132,0.06301154150598019,0.2927214411347109,0.06080741401107928,1.2870000000000008,-1.334736494330224,0.08756709405749778,-1.3047493853477974,0.06080445362765088 +24 pose 2,14 docked,1.5576703380274326,0.06661791257181175,-10.100546752316397,0.06328979223511295,2.3072,11.658217090343829,0.09188875925046174,11.764003063648412,0.06627066120337696 +24 pose 2,16 docked,-1.5746552723974612,0.07325462816115093,-12.20316898305241,0.07446495960187631,1.3957000000000015,10.62851371065495,0.10445702827257512,10.108183379881181,0.06190434593809108 +24 pose 2,20,13.906764570710692,0.05549464919259727,4.963954107463382,0.056605237829383204,3.0950000000000006,8.942810463247309,0.07927048024788592,9.163741622969754,0.07001623305755421 diff --git a/summaries/2026_june_08/water_set/chk1/dg_comparison_plot.png b/summaries/2026_june_08/water_set/chk1/dg_comparison_plot.png new file mode 100644 index 0000000..6cd3fc4 Binary files /dev/null and b/summaries/2026_june_08/water_set/chk1/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/water_set/chk1/dg_plot.png b/summaries/2026_june_08/water_set/chk1/dg_plot.png new file mode 100644 index 0000000..65b684c Binary files /dev/null and b/summaries/2026_june_08/water_set/chk1/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/chk1/dg_results.csv b/summaries/2026_june_08/water_set/chk1/dg_results.csv new file mode 100644 index 0000000..2cf9c5e --- /dev/null +++ b/summaries/2026_june_08/water_set/chk1/dg_results.csv @@ -0,0 +1,14 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +13 docked,c1cc(-c2ccc3c(-c4cc5cc(C[NH+]6CCOCC6)ccc5[nH]4)n[nH]c3c2)[nH]n1,-11.343991937479917,0.04661691696355663,-9.92085 +12 docked,Cn1cc(-c2ccc3c(-c4cc5cc(C[NH+]6CCOCC6)ccc5[nH]4)n[nH]c3c2)cn1,-11.649475486972278,0.04827863416302417,-8.61243 +11 docked,c1cc2[nH]c(-c3n[nH]c4cc(-c5cn[nH]c5)ccc34)cc2cc1C[NH+]1CCCCC1,-9.031749297016498,0.05539018091530315,-10.9787 +14 docked,c1cc2[nH]c(-c3n[nH]c4cc(-c5cnsc5)ccc34)cc2cc1C[NH+]1CCCCC1,-8.45235973768598,0.04294467153091261,-10.8701 +16 docked,c1cn(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)nn1,-10.10817942145321,0.03584120983711428,-11.7816 +17 torsion adjust,Cc1cnnn1-c1ccc2c(-c3cc4cc(C[NH+]5CCCCC5)ccc4[nH]3)n[nH]c2c1,-10.569033419650255,0.04818653358083987,-10.3239 +19,c1cnn(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)n1,-10.003532165815137,0.042319797373124475,-10.2494 +15 docked,c1csc(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)n1,-10.537245309380115,0.049887220400980356,-10.0438 +18 docked,c1cnn(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)c1,-11.23032880277669,0.04070342774541978,-9.54958 +20,c1ccc(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)cc1,-11.052621178364637,0.04852542805720471,-10.0823 +21 (Xtal),OCc1nn[nH]c1-c1ccc2c(-c3cc4cc(C[NH+]5CCCCC5)ccc4[nH]3)n[nH]c2c1,-8.72885040596548,0.05201270857701987,-13.0686 +22,OCc1nn[nH]c1-c1ccc2c(-c3cc4cc(C[N@H+]5CC[C@H](F)CC5)ccc4[nH]3)n[nH]c2c1,-8.803430036105413,0.049118115378840504,-13.0686 +24 pose 2,COc1cc(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)ccc1O,-20.21636280133439,0.050473316945043305,-13.1773 diff --git a/summaries/2026_june_08/water_set/hsp90_kung/README.md b/summaries/2026_june_08/water_set/hsp90_kung/README.md new file mode 100644 index 0000000..226f02b --- /dev/null +++ b/summaries/2026_june_08/water_set/hsp90_kung/README.md @@ -0,0 +1,40 @@ +# Hsp90 Kung Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 2.04 +- RMSE: 2.61 +- R²: 0.53 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.78 + +## System Details +- Ligands: 11 +- Host Atoms: 3924 +- Map Details: + - Edges: 18 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.6 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.51 Hours +- Average Time Per Edge: 0.08 Hours +- Total Nanoseconds Simulated: 1781.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/hsp90_kung/ddg_results.csv b/summaries/2026_june_08/water_set/hsp90_kung/ddg_results.csv new file mode 100644 index 0000000..a920e48 --- /dev/null +++ b/summaries/2026_june_08/water_set/hsp90_kung/ddg_results.csv @@ -0,0 +1,19 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +cmpd 11,cmpd 10,-3.1685648077985213,0.04651324857026449,-5.321192002670957,0.04230642048793578,0.0,2.152627194872436,0.06287539667518006,2.4096608422290213,0.05839189829434838 +cmpd 11,cmpd 8,-10.023034109582765,0.0634454780491152,-19.871332926340962,0.06309065106394444,2.329999999999999,9.848298816758197,0.08947490674235517,9.511480128471426,0.06071956978106511 +cmpd 12,cmpd 10,-4.02548075285577,0.046470570426222976,-6.8483316484408,0.04636724968172378,0.0,2.82285089558503,0.06564629280306591,2.7398426183008713,0.05481504383987209 +cmpd 12,cmpd 8,-12.732015923986804,0.06684489129891111,-21.91764620100168,0.06645182021046114,2.329999999999999,9.185630277014877,0.09425541842274478,9.841661904543276,0.05728823089559678 +cmpd 13,cmpd 10,3.611684116068928,0.056282155658342214,0.2598271464455312,0.0546173642645314,0.9600000000000009,3.351856969623397,0.07842663785190829,3.0704284163095092,0.05917137399388212 +cmpd 13,cmpd 12,5.222205210193641,0.04485396588323176,4.882822074061559,0.04250723597498637,0.9600000000000009,0.3393831361320821,0.061795981792405356,0.33058579800863797,0.0537123807831754 +cmpd 14,cmpd 17,-5.3377905339992235,0.05539978120124357,-1.6290185733850013,0.055050920334654856,-2.919999999999999,-3.708771960614222,0.07810082961683683,-3.324820523393514,0.06459300500370367 +cmpd 15,cmpd 11,-1.2275435550780673,0.05372480959904928,-2.444972319665402,0.05263610372222447,0.41999999999999993,1.2174287645873347,0.07521246294006646,0.9348890217983445,0.055081708424025703 +cmpd 15,cmpd 12,-0.4985527035455071,0.043460379650632354,-0.8708949694587393,0.04686149413075742,0.41999999999999993,0.37234226591323216,0.06391247320784973,0.6047072457264946,0.051274456093253276 +cmpd 15,cmpd 17,-1.4817633221645325,0.05567284388896685,-1.3785336243511352,0.052130866050047325,-1.1300000000000008,-0.10322969781339723,0.0762698678497167,-0.424845837657605,0.06164801423343902 +cmpd 16,cmpd 14,5.342217732649429,0.04674487347221134,3.07654275978577,0.04855402282533073,2.509999999999999,2.265674972863659,0.0673986374376796,2.5200875793749713,0.05978519348107068 +cmpd 16,cmpd 15,2.871258081986989,0.043831275052303685,3.06936522134856,0.04287866516405147,0.7200000000000006,-0.1981071393615711,0.06131688673572347,-0.3798871063609379,0.056590553302533354 +cmpd 16,cmpd 17,0.9231940126011979,0.04176925750579798,1.7007683058297833,0.04245042119918199,-0.41000000000000014,-0.7775742932285853,0.059554253690006234,-0.8047329440185429,0.06429063747494895 +cmpd 7,cmpd 8,52.430956832527755,0.043057071605698445,49.361961530457464,0.04030235759040581,2.55,3.0689953020702916,0.058976193863313896,2.958488202541484,0.06517703243668126 +cmpd 7,cmpd 11,61.901831987984856,0.06353818944434994,69.03881635926977,0.06304559780578536,0.22000000000000064,-7.13698437128491,0.08950893207135784,-6.552991925929943,0.06131464991007839 +cmpd 9,cmpd 13,-8.951860384846485,0.04703821219330318,-5.625511735940922,0.04882458880463165,-2.2299999999999995,-3.3263486489055625,0.06779700493593782,-3.547248568786854,0.05842345218000595 +cmpd 9,cmpd 14,-0.5776861524103024,0.043664330042080035,0.37160538957780326,0.04597231343092435,0.09999999999999964,-0.9492915419881057,0.06340368538353934,-0.9213953307688012,0.05940646765608739 +cmpd 9,cmpd 7,-68.09361325290936,0.06271520074261895,-71.43628959787009,0.06278711217749829,-1.4899999999999993,3.3426763449607164,0.0887435510883847,3.666510931223577,0.06231245022928935 diff --git a/summaries/2026_june_08/water_set/hsp90_kung/dg_comparison_plot.png b/summaries/2026_june_08/water_set/hsp90_kung/dg_comparison_plot.png new file mode 100644 index 0000000..e48a56e Binary files /dev/null and b/summaries/2026_june_08/water_set/hsp90_kung/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/water_set/hsp90_kung/dg_plot.png b/summaries/2026_june_08/water_set/hsp90_kung/dg_plot.png new file mode 100644 index 0000000..9186f02 Binary files /dev/null and b/summaries/2026_june_08/water_set/hsp90_kung/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/hsp90_kung/dg_results.csv b/summaries/2026_june_08/water_set/hsp90_kung/dg_results.csv new file mode 100644 index 0000000..31e67ff --- /dev/null +++ b/summaries/2026_june_08/water_set/hsp90_kung/dg_results.csv @@ -0,0 +1,12 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 11,COc1cc(-c2nc(C)nc3[nH]cc(F)c23)c(Cl)cc1Cl,-10.899556764402753,0.03998941666704399,-9.19 +cmpd 10,COc1cc(-c2nc(C)nc3[nH]cc(C(C)=O)c23)c(Cl)cc1Cl,-8.489895922173732,0.0425495045922637,-9.19 +cmpd 8,COc1cc(-c2cc(C)nc(N)c2)c(Cl)cc1Cl,-1.3880766359313261,0.04569149493097353,-6.86 +cmpd 12,COc1cc(-c2nc(C)nc3[nH]cc(Cl)c23)c(Cl)cc1Cl,-11.229738540474603,0.03455761406868289,-9.19 +cmpd 13,COc1cc(-c2nc(C)nc3[nH]cc(C#N)c23)c(Cl)cc1Cl,-11.560324338483241,0.04111923101514424,-10.15 +cmpd 14,COc1cc(-c2nc(C)nc3[nH]c(C)cc23)c(Cl)cc1Cl,-8.934471100465188,0.042504350295247614,-7.820000000000001 +cmpd 17,CCc1[nH]c2nc(C)nc(-c3cc(OC)c(Cl)cc3Cl)c2c1C#N,-12.259291623858703,0.04863780938105017,-10.74 +cmpd 15,COc1cc(-c2nc(C)nc3[nH]c(C)c(Cl)c23)c(Cl)cc1Cl,-11.834445786201098,0.0378792972154834,-9.61 +cmpd 16,COc1cc(-c2nc(C)nc3[nH]c(C)c(C#N)c23)c(Cl)cc1Cl,-11.45455867984016,0.042043424759978104,-10.33 +cmpd 7,COc1cc(-c2cc(C)nc(N)n2)c(Cl)cc1Cl,-4.34656483847281,0.04647938089330602,-9.41 +cmpd 9,COc1cc(-c2nc(C)nc3[nH]ccc23)c(Cl)cc1Cl,-8.013075769696387,0.04150311561018813,-7.920000000000001 diff --git a/summaries/2026_june_08/water_set/hsp90_woodhead/README.md b/summaries/2026_june_08/water_set/hsp90_woodhead/README.md new file mode 100644 index 0000000..cc5db85 --- /dev/null +++ b/summaries/2026_june_08/water_set/hsp90_woodhead/README.md @@ -0,0 +1,40 @@ +# Hsp90 Woodhead Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.30 +- RMSE: 1.41 +- R²: 0.51 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.60 + +## System Details +- Ligands: 4 +- Host Atoms: 4042 +- Map Details: + - Edges: 6 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 5.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.55 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 631.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/hsp90_woodhead/ddg_results.csv b/summaries/2026_june_08/water_set/hsp90_woodhead/ddg_results.csv new file mode 100644 index 0000000..3329362 --- /dev/null +++ b/summaries/2026_june_08/water_set/hsp90_woodhead/ddg_results.csv @@ -0,0 +1,7 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +1,2,8.618704628016086,0.04889935177643263,11.045158757102222,0.04084708514563817,1.9800000000000004,-2.426454129086136,0.06371523341439095,-1.628841533493853,0.04826275272447626 +1,3,24.326274200865917,0.05832184300412206,21.37420668540476,0.059245494273773666,4.640000000000001,2.9520675154611533,0.08313522696872373,2.4249957229432297,0.04821722409106477 +3,2,-13.34946537402752,0.06239033372155736,-10.119506500041057,0.0633221068330666,-2.66,-3.2299588739864635,0.08889456088909825,-4.053837256437083,0.04239755785659193 +4,1,-26.037350217284654,0.05983912692804782,-22.00654754282359,0.059462204783341674,-3.790000000000001,-4.030802674461063,0.08435920168663925,-3.1753051007057334,0.047801690321683084 +4,3,-1.6287952793944571,0.031773000253642464,-0.939248266910466,0.034068928712249494,0.8499999999999996,-0.6895470124839912,0.046585571250316364,-0.7503093777625036,0.04187196209003359 +4,2,-15.459815593324747,0.0638667769415188,-11.407897298416037,0.06386183949165761,-1.8100000000000005,-4.051918294908708,0.09031777089895408,-4.804146634199586,0.04192438205585377 diff --git a/summaries/2026_june_08/water_set/hsp90_woodhead/dg_comparison_plot.png b/summaries/2026_june_08/water_set/hsp90_woodhead/dg_comparison_plot.png new file mode 100644 index 0000000..b078143 Binary files /dev/null and b/summaries/2026_june_08/water_set/hsp90_woodhead/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/water_set/hsp90_woodhead/dg_plot.png b/summaries/2026_june_08/water_set/hsp90_woodhead/dg_plot.png new file mode 100644 index 0000000..e63b9fa Binary files /dev/null and b/summaries/2026_june_08/water_set/hsp90_woodhead/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/hsp90_woodhead/dg_results.csv b/summaries/2026_june_08/water_set/hsp90_woodhead/dg_results.csv new file mode 100644 index 0000000..1909eb8 --- /dev/null +++ b/summaries/2026_june_08/water_set/hsp90_woodhead/dg_results.csv @@ -0,0 +1,5 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1,CC(C)c1cc(C(=O)N2Cc3ccccc3C2)c(O)cc1O,-11.110364822538777,0.037793128260232955,-12.72 +2,COc1cc(O)c(C(=O)N2Cc3ccccc3C2)cc1C(C)C,-12.73920635603263,0.030016208235710287,-10.74 +3,CC1(C)COc2cc(O)c(C(=O)N3Cc4ccccc4C3)cc21,-8.685369099595547,0.029942948341029115,-8.08 +4,CC1(C)CNc2cc(O)c(C(=O)N3Cc4ccccc4C3)cc21,-7.935059721833044,0.029269114334322992,-8.93 diff --git a/summaries/2026_june_08/water_set/scyt_dehyd/README.md b/summaries/2026_june_08/water_set/scyt_dehyd/README.md new file mode 100644 index 0000000..ef78084 --- /dev/null +++ b/summaries/2026_june_08/water_set/scyt_dehyd/README.md @@ -0,0 +1,40 @@ +# Scyt Dehyd Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 2.10 +- RMSE: 2.63 +- R²: 0.64 +- Kendall 𝜏: 0.52 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 7 +- Host Atoms: 3060 +- Map Details: + - Edges: 11 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 3 + - Mean Dummy Atoms: 1.8 + - Median Dummy Atoms: 2.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.74 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 862.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/scyt_dehyd/ddg_results.csv b/summaries/2026_june_08/water_set/scyt_dehyd/ddg_results.csv new file mode 100644 index 0000000..853e528 --- /dev/null +++ b/summaries/2026_june_08/water_set/scyt_dehyd/ddg_results.csv @@ -0,0 +1,12 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +2d,4d,40.50597962015577,0.05181596550520119,47.75573936116595,0.05150237237662355,-1.8617000000000026,-7.24975974101018,0.07305743385622435,-7.09061722825008,0.055708001448617726 +2d,7d,65.14084540110886,0.05409942327537366,75.17449007867165,0.05549676929795141,-1.7698,-10.033644677562792,0.07750250964477269,-10.385281358713216,0.056512042875750255 +3d,5d,-27.00128027425044,0.04396598271585848,-19.828153896715644,0.0442332335670497,-4.060230000000001,-7.173126377534795,0.06236655023302426,-7.3380528689699345,0.04602273783832093 +3d,4d,-5.412677791751043,0.052359447798477385,4.625297660097103,0.051437986293769875,-6.1501300000000025,-10.037975451848146,0.07339876162252015,-9.743723819866652,0.04957475743930975 +3d,6d,15.41322534441064,0.03619173631081167,20.00496613766592,0.04006173495540377,-0.2125799999999991,-4.591740793255282,0.0539887431306596,-4.627349679676583,0.047870312344669035 +4d,7d,23.974714237022184,0.04155556092130876,27.56004382546615,0.04141981241618462,0.09190000000000254,-3.585329588443964,0.058672527677581146,-3.2946641304631363,0.05124141235031798 +5d,6d,42.77697707769313,0.03936082810539775,39.86361723326288,0.03958466519980054,3.8476500000000016,2.913359844430256,0.055823118043718846,2.7107031892933513,0.045053288746128996 +5d,7d,45.69247735126672,0.05233387340310049,51.25534761594276,0.05069451649778884,-1.9979999999999993,-5.562870264676042,0.07286129499477988,-5.700335081359853,0.04781336803263016 +8d,2d,-48.94638710505817,0.043801434345850286,-50.28559208122923,0.04421255025240807,-2.853300000000001,1.3392049761710643,0.06223596428573709,1.227944816766465,0.052788815401125594 +8d,5d,-30.113768109597423,0.0379909540144366,-26.80592290554725,0.04037956407605604,-2.6251000000000015,-3.3078452040501745,0.05544205787936944,-3.4570014605868984,0.043349350676650494 +8d,6d,12.156933609822474,0.04212175738025011,13.20129233560688,0.04565272463451893,1.22255,-1.0443587257844062,0.062116130846631666,-0.7462982712935471,0.0453060769646697 diff --git a/summaries/2026_june_08/water_set/scyt_dehyd/dg_comparison_plot.png b/summaries/2026_june_08/water_set/scyt_dehyd/dg_comparison_plot.png new file mode 100644 index 0000000..d1aff34 Binary files /dev/null and b/summaries/2026_june_08/water_set/scyt_dehyd/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/water_set/scyt_dehyd/dg_plot.png b/summaries/2026_june_08/water_set/scyt_dehyd/dg_plot.png new file mode 100644 index 0000000..2c4e9f3 Binary files /dev/null and b/summaries/2026_june_08/water_set/scyt_dehyd/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/scyt_dehyd/dg_results.csv b/summaries/2026_june_08/water_set/scyt_dehyd/dg_results.csv new file mode 100644 index 0000000..c53479c --- /dev/null +++ b/summaries/2026_june_08/water_set/scyt_dehyd/dg_results.csv @@ -0,0 +1,8 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2d,c1ccc(C(CCNc2ncnc3ccccc23)c2ccccc2)cc1,-9.121099117496206,0.042844545018791536,-13.4817 +4d,N#Cc1cnc2ccccc2c1NCCC(c1ccccc1)c1ccccc1,-16.211716345746286,0.03560514552044325,-15.343400000000003 +7d,N#Cc1nnc2ccccc2c1NCCC(c1ccccc1)c1ccccc1,-19.506380476209422,0.036850453893044255,-15.2515 +3d,c1ccc(C(CCNc2ccnc3ccccc23)c2ccccc2)cc1,-6.467992525879635,0.03449536472679276,-9.19327 +5d,c1ccc(C(CCNc2nnnc3ccccc23)c2ccccc2)cc1,-13.80604539484957,0.030465754717393087,-13.2535 +6d,c1ccc(C(CCNc2cnnc3ccccc23)c2ccccc2)cc1,-11.095342205556218,0.03319091165276595,-9.40585 +8d,c1ccc(C(CCNc2nncc3ccccc23)c2ccccc2)cc1,-10.34904393426267,0.030838352640613922,-10.6284 diff --git a/summaries/2026_june_08/water_set/taf12/README.md b/summaries/2026_june_08/water_set/taf12/README.md new file mode 100644 index 0000000..02ca521 --- /dev/null +++ b/summaries/2026_june_08/water_set/taf12/README.md @@ -0,0 +1,40 @@ +# Taf12 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.63 +- RMSE: 0.78 +- R²: 0.14 +- Kendall 𝜏: 0.29 +- Spearman ρ: 0.29 + +## System Details +- Ligands: 8 +- Host Atoms: 2702 +- Map Details: + - Edges: 13 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.93 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 1127.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/taf12/ddg_results.csv b/summaries/2026_june_08/water_set/taf12/ddg_results.csv new file mode 100644 index 0000000..252ba64 --- /dev/null +++ b/summaries/2026_june_08/water_set/taf12/ddg_results.csv @@ -0,0 +1,14 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +cmpd 2 (methyl),cmpd 6 (ethyl),4.2543673804606685,0.04405563602978386,3.946764898050208,0.045288131277659065,1.33,0.3076024824104611,0.06318159463491936,0.19669701686775642,0.0527630225631831 +cmpd 2 (methyl),cmpd 3 (Allyl),4.956500311420757,0.053149660593948905,5.76098236610595,0.05117057178458801,1.5199999999999996,-0.8044820546851937,0.07377881700063806,-0.5137311578983006,0.05179949854194914 +cmpd 2 (methyl),cmpd 7 (n-propyl),6.295702069067745,0.0531662049584537,6.371763939462334,0.04966840998447253,1.7400000000000002,-0.07606187039458942,0.07275710480819009,-0.21174621195739896,0.0545769099886198 +cmpd 3 (Allyl),cmpd 4 (Crotyl),4.053410233221996,0.03990702878528829,5.1426167601615385,0.041054839114048065,-0.370000000000001,-1.0892065269395426,0.05725443878993312,-0.6923322411517177,0.04995547705979142 +cmpd 3 (Allyl),cmpd 6 (ethyl),1.385716801768224,0.047740848079904495,0.6317022995582248,0.04899209650468196,-0.1899999999999995,0.7540145022099992,0.06840624310187332,0.710428174766057,0.048898453623841695 +cmpd 3 (Allyl),cmpd 8 (n-Butyl),12.940676051469993,0.05676832134418948,13.012728780182778,0.05696477014345923,0.0600000000000005,-0.0720527287127853,0.08042156020455152,-0.44937842052271293,0.04976736083896219 +cmpd 5 (1-Butenyl),cmpd 7 (n-propyl),0.3827189967657939,0.04448128382236971,-0.7765280496908445,0.04654424503849976,1.8800000000000008,1.1592470464566382,0.06438129663722314,1.4192548795834306,0.05683856501895615 +cmpd 5 (1-Butenyl),cmpd 8 (n-Butyl),9.652824948618562,0.053004306612584866,8.66878744233061,0.05162586675503905,1.7200000000000006,0.984037506287953,0.07399112539818511,0.667891513119816,0.055871740241231406 +cmpd 5 (1-Butenyl),cmpd 9 (methoxyethyl),-5.48590364301327,0.04934679235506794,-7.075388486044736,0.04878690122359217,2.3099999999999987,1.5894848430314665,0.06939212957342303,1.5654954855182446,0.05793667112411227 +cmpd 6 (ethyl),cmpd 7 (n-propyl),2.731160211193941,0.0436417807786332,3.005047627405641,0.04150335253096558,0.41000000000000014,-0.2738874162117,0.060225686387453355,-0.4084432288251554,0.051831552374123555 +cmpd 8 (n-Butyl),cmpd 4 (Crotyl),-9.064331558073091,0.053853172810202896,-8.922802961990811,0.053599438016785725,-0.4300000000000015,-0.14152859608227975,0.07598068160684551,-0.24295382062900472,0.05178831554655349 +cmpd 9 (methoxyethyl),cmpd 4 (Crotyl),6.22073662508922,0.05034699916885568,6.812001790752539,0.05265278107838995,-1.0199999999999996,-0.5912651656633198,0.07285009046389451,-1.1405577930274333,0.05400959294893179 +cmpd 9 (methoxyethyl),cmpd 8 (n-Butyl),12.844190809261034,0.04254854485154829,14.081933545078236,0.040523408363435126,-0.5899999999999981,-1.2377427358172006,0.058758193423334076,-0.8976039723984286,0.05383564476360827 diff --git a/summaries/2026_june_08/water_set/taf12/dg_plot.png b/summaries/2026_june_08/water_set/taf12/dg_plot.png new file mode 100644 index 0000000..8d6913a Binary files /dev/null and b/summaries/2026_june_08/water_set/taf12/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/taf12/dg_results.csv b/summaries/2026_june_08/water_set/taf12/dg_results.csv new file mode 100644 index 0000000..c2b2985 --- /dev/null +++ b/summaries/2026_june_08/water_set/taf12/dg_results.csv @@ -0,0 +1,9 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 2 (methyl),CN(C)C(=O)c1cccc(-c2cn(C)c(=O)c3[nH]ccc23)c1,-8.141942496497201,0.03921776276381254,-9.86 +cmpd 6 (ethyl),CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.9452454796294445,0.0352973601534773,-8.53 +cmpd 3 (Allyl),C=CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.655673654395502,0.03384014085370671,-8.34 +cmpd 7 (n-propyl),CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.3536887084546,0.03795531830596637,-8.12 +cmpd 4 (Crotyl),C/C=C/Cn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.34800589554722,0.0367477149666838,-8.71 +cmpd 8 (n-Butyl),CCCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.105052074918214,0.03649157535482344,-8.28 +cmpd 5 (1-Butenyl),C=CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.77294358803803,0.04230858406643833,-10.0 +cmpd 9 (methoxyethyl),COCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.207448102519786,0.03958082332691761,-7.690000000000001 diff --git a/summaries/2026_june_08/water_set/thrombin/README.md b/summaries/2026_june_08/water_set/thrombin/README.md new file mode 100644 index 0000000..9a7a396 --- /dev/null +++ b/summaries/2026_june_08/water_set/thrombin/README.md @@ -0,0 +1,40 @@ +# Thrombin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.93 +- RMSE: 1.14 +- R²: 0.29 +- Kendall 𝜏: 0.35 +- Spearman ρ: 0.50 + +## System Details +- Ligands: 21 +- Host Atoms: 5256 +- Map Details: + - Edges: 37 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 3.5 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.66 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 2967.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/thrombin/ddg_results.csv b/summaries/2026_june_08/water_set/thrombin/ddg_results.csv new file mode 100644 index 0000000..9124c88 --- /dev/null +++ b/summaries/2026_june_08/water_set/thrombin/ddg_results.csv @@ -0,0 +1,38 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +1a pose 2,2a pose 2,2.501107999281864,0.03851872118374196,4.614347382389451,0.03757937059637367,0.7928199999999999,-2.1132393831075875,0.053813576131404285,-2.118502488684997,0.050055726819551574 +1a pose 2,1d pose 2,-0.18931322497229303,0.06030664487197835,2.69250842561699,0.06044773820009287,-1.1919900000000005,-2.8818216505892833,0.08538630141434796,-2.649864840692614,0.05377473427364192 +1a pose 2,6b pose 2,1.713324726964008,0.054033044319940875,4.950580732812462,0.05322402665058056,-1.6275999999999993,-3.2372560058484536,0.07584435965437644,-3.307092985408123,0.05282855718130313 +1a pose 2,6d pose 2,-15.645391886656519,0.05040241853049126,-13.807411836191548,0.05152275801929071,-1.3236100000000004,-1.8379800504649715,0.0720763372240654,-2.107886506984321,0.06026482455839769 +1b pose 2,1d pose 2,-0.6894826070879905,0.04303153779501062,1.043331293265466,0.043274971648384404,0.6547699999999992,-1.7328139003534564,0.061028160845399075,-1.8640206642805506,0.058244391810303366 +1c pose 2,1d pose 2,-0.5766970803278666,0.035257962260941085,0.737455907911223,0.036718279267726084,-0.0216700000000003,-1.3141529882390897,0.050905362538505396,-1.3053068464819297,0.0623784637206135 +1c pose 2,2a pose 2,1.740426983994889,0.043009108486776346,2.590227332928278,0.0438986393420156,1.96314,-0.8498003489333893,0.06145627672506412,-0.7739444944743124,0.05920241952299476 +2a pose 2,1b pose 2,-1.695907311632361,0.03820357585898476,-2.9777196024018378,0.036386786800799945,-2.6395799999999996,1.2818122907694764,0.05275899413465037,1.3326583122729332,0.05482939830588067 +2b pose 1,3a xtal pose,0.09699569003363967,0.041879782392552724,-0.7678227017876844,0.040461282544520624,-0.8348000000000004,0.8648183918213241,0.05823256441541192,0.9197909029982938,0.07783353690474985 +2b pose 1,3b pose 1,8.47702664765337,0.04268037908285236,7.904495264793525,0.04204792285865852,0.030750000000000277,0.5725313828598453,0.05991362595757062,0.5345327252407204,0.08302992912351936 +2b pose 1,6a pose 1,-4.793771410470682,0.05699297426579415,-3.076549189168455,0.05612144620016268,-2.6252000000000004,-1.7172222213022268,0.07998634783048435,-2.0672880036691605,0.07774644162195234 +2b pose 1,7e pose 1,-6.371936653971594,0.051000374006032086,-6.306979516911243,0.04937365459835652,1.63091,-0.06495713706035071,0.07098447659279432,0.18240210476059104,0.07989053607220138 +2c pose 2,1a pose 2,16.663390123635534,0.029996634847035342,15.951670340734614,0.028407978214367434,-0.1236600000000001,0.7117197829009204,0.04131357317364778,1.1115541423848248,0.045570375593905525 +2c pose 2,1b pose 2,18.14472327720714,0.04469009262470845,17.626328735083504,0.043907346316969416,-1.9704199999999998,0.518394542123636,0.06265029480699438,0.32570996597276114,0.050767570977159775 +2d pose 2,1a pose 2,15.567263864036097,0.030396550933110483,14.82075118370778,0.030610962279542072,-0.7784300000000002,0.7465126803283169,0.043139092715409846,0.2826391873773879,0.047992069830185585 +2d pose 2,2c pose 2,-3.7183615094268796,0.03711201410929021,-2.3936917282957078,0.036055987315378436,-0.6547700000000001,-1.3246697811311718,0.05174297838871363,-0.8289149550074368,0.05205940434603366 +2d pose 2,7a pose 2,24.790281180514643,0.05405758112621079,27.21104403958041,0.053321502047400736,-0.9937900000000006,-2.4207628590657686,0.07593026180521059,-2.0512256494121024,0.06157475360099932 +3b pose 1,3a xtal pose,-2.281626892695659,0.04309594976561607,-2.699061423782572,0.042358007660060676,-0.8655500000000007,0.41743453108691325,0.06042732576517236,0.38525817775757343,0.08208430309078128 +5,1b pose 2,-4.445794778004804,0.04167466443428201,-1.9547831539260236,0.04223968515505763,-2.4624299999999995,-2.4910116240787805,0.05933775069640242,-2.547694893905377,0.05192914463043098 +5,1c pose 2,-4.518703591221715,0.0428108077636439,-1.3235477271256335,0.04409115055257637,-1.78599,-3.195155864096081,0.06145563292673527,-3.106408711703998,0.05652698135262469 +5,3a xtal pose,-1.5644445671362837,0.04563477316197351,0.03636005544328306,0.04546924204968704,-1.32681,-1.6008046225795667,0.06442037328452704,-1.631511336052788,0.06566621922666256 +6a pose 1,6c pose 1,5.274664563746641,0.04728536727346064,4.756155990363904,0.048512993444621844,0.8964300000000005,0.5185085733827363,0.06774523223920621,0.5944700181350218,0.07639379235509673 +6a pose 1,6e pose 1,3.0005283715312108,0.04209847450958206,2.087728133443337,0.041339245809256735,1.2636800000000008,0.9128002380878738,0.05900182031185208,0.8294227959747875,0.07292077393096405 +6c pose 1,6e pose 1,-2.6251579421215103,0.03893147470055405,-2.6349762820564813,0.038226267368216826,0.3672500000000003,0.009818339934970843,0.05456104140562457,0.23495277783976576,0.07265416846123542 +6d pose 2,6b pose 2,23.691644299995982,0.04303481583456728,24.67662084751344,0.04538403046155974,-0.30398999999999887,-0.984976547517459,0.06254362953051978,-1.1992064784238021,0.06894192639766795 +7a pose 2,6b pose 2,-2.4068529416430384,0.03273554550289176,-1.2918289417211246,0.03236794260637337,-1.4122399999999988,-1.1150239999219138,0.04603585176730607,-0.9732281486186327,0.06541458528720169 +7a pose 2,6d pose 2,-25.60066917646458,0.0482295508524268,-25.839520947127593,0.04746647074304297,-1.10825,0.23885177066301172,0.06766945707057931,0.2259783298051694,0.0715545986886435 +7b,1a pose 2,-4.015409718168603,0.04802169761762372,-3.278181789037285,0.04863265655004821,0.0,-0.7372279291313178,0.06834631464236704,-1.0086723019540837,0.048075830216018224 +7b,7f,-10.90709626083912,0.04181173060477737,-8.91717259066163,0.039657688521858234,1.28653,-1.98992367017749,0.05762771099968489,-1.83577893114622,0.06136487717261136 +7b,1b pose 2,-3.0803327563099083,0.049651806085915316,-1.2274901083649885,0.05022283739565492,-1.8467599999999997,-1.8528426479449196,0.07062319196739646,-1.7945164783661474,0.05302803581230165 +7c pose 1,1a pose 2,-4.5860859047065246,0.0496874659136328,-4.475424764606942,0.048844483721346255,0.5991900000000001,-0.11066114009958287,0.06967515955434389,0.2596235426882494,0.05014137911711151 +7c pose 1,6c pose 1,-0.25463521731894534,0.05408815263441202,2.107562557480946,0.056220812534550794,-1.0059199999999997,-2.3621977747998915,0.07801479358075977,-2.0026459644036576,0.0676601800047009 +7c pose 1,6e pose 1,-2.08012543641191,0.0507416248576002,-0.5790549634218967,0.05084060185706918,-0.6386699999999994,-1.5010704729900133,0.07182951545415336,-1.7676931865638918,0.06371285363696762 +7c pose 1,7f,-10.59788921037447,0.0558613018059199,-10.551474383613144,0.05573948774112047,1.88572,-0.04641482676132653,0.0789137220836439,-0.5674830865038869,0.0629961951169765 +7e pose 1,3b pose 1,14.888387619500646,0.05044710544269246,14.545200415898233,0.049972458437327935,-1.6001599999999998,0.34318720360241284,0.07100814777063684,0.35213062048012933,0.08403731969012279 +7e pose 1,6a pose 1,1.801303898520146,0.050317571100661256,4.29175738539154,0.0505611005278848,-4.2561100000000005,-2.4904534868713935,0.0713322006394095,-2.2496901084297516,0.07882138767694269 +7f,1a pose 2,6.818099462779559,0.05457855861564729,5.777745884782315,0.05238990097185326,-1.28653,1.040353577997244,0.07565395418880787,0.8271066291921363,0.05589346130757576 diff --git a/summaries/2026_june_08/water_set/thrombin/dg_plot.png b/summaries/2026_june_08/water_set/thrombin/dg_plot.png new file mode 100644 index 0000000..4f68abd Binary files /dev/null and b/summaries/2026_june_08/water_set/thrombin/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/thrombin/dg_results.csv b/summaries/2026_june_08/water_set/thrombin/dg_results.csv new file mode 100644 index 0000000..ca15432 --- /dev/null +++ b/summaries/2026_june_08/water_set/thrombin/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(F)c1,-6.712886170181908,0.028893912139853973,-7.4093 +2a pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(C(F)(F)F)c1,-8.831388658866905,0.040874412884932966,-6.61648 +1d pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(I)c1,-9.362751010874522,0.04535266130510092,-8.60129 +6b pose 2,Cc1ccc(Cl)cc1CNC(=O)[C@@H]1CCCN1C(=O)[C@H]([NH3+])Cc1ccccc1,-10.01997915559003,0.0442266695005696,-9.0369 +6d pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1O,-8.820772677166229,0.05288658544762417,-8.73291 +1b pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(Cl)c1,-7.498730346593971,0.036545113078179634,-9.25606 +1c pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(Br)c1,-8.057444164392592,0.04282766452526564,-8.57962 +2b pose 1,COc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-7.502337691739676,0.05574134813341197,-7.28564 +3a xtal pose,Cc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-6.582546788741382,0.05432275375358678,-8.12044 +3b pose 1,CCc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-6.967804966498956,0.06153755957564794,-7.25489 +6a pose 1,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1Cl,-9.569625695408837,0.05419789011710154,-9.91084 +7e pose 1,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(CO)c1,-7.319935586979085,0.05723110921669682,-5.65473 +2c pose 2,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(O)c1,-7.824440312566733,0.03523919654339496,-7.28564 +2d pose 2,Nc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-6.995525357559296,0.038319454691315855,-6.63087 +7a pose 2,Cc1ccc(C)c(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-9.046751006971398,0.04819823309192953,-7.62466 +5,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1ccccc1,-4.951035452688594,0.036892963721437216,-6.79363 +6c pose 1,COc1ccc(Cl)cc1CNC(=O)[C@@H]1CCCN1C(=O)[C@H]([NH3+])Cc1ccccc1,-8.975155677273815,0.053838649846074546,-9.01441 +6e pose 1,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1F,-8.740202899434049,0.04878553041164309,-8.64716 +7b,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1ccc(Cl)cc1,-5.704213868227824,0.03842430600822623,-7.4093 +7f,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1ccc(CO)cc1,-7.539992799374044,0.04784580293187552,-6.12277 +7c pose 1,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1ccccc1Cl,-6.972509712870157,0.04097925988863519,-8.00849 diff --git a/summaries/2026_june_08/water_set/urokinase/README.md b/summaries/2026_june_08/water_set/urokinase/README.md new file mode 100644 index 0000000..f467167 --- /dev/null +++ b/summaries/2026_june_08/water_set/urokinase/README.md @@ -0,0 +1,40 @@ +# Urokinase Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.69 +- RMSE: 0.73 +- R²: 0.59 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.80 + +## System Details +- Ligands: 4 +- Host Atoms: 4581 +- Map Details: + - Edges: 6 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 3 + - Mean Dummy Atoms: 1.8 + - Median Dummy Atoms: 2.0 + +## Simulation Details +- TMD Sha: [7bfbc5dc44e1a1030ec36835a3e6d1725546d398](https://github.com/tmd-industries/tmd/tree/7bfbc5dc44e1a1030ec36835a3e6d1725546d398) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 0.42 Hours +- Average Time Per Edge: 0.07 Hours +- Total Nanoseconds Simulated: 458.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 608 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_june_08/water_set/urokinase/ddg_results.csv b/summaries/2026_june_08/water_set/urokinase/ddg_results.csv new file mode 100644 index 0000000..f3232be --- /dev/null +++ b/summaries/2026_june_08/water_set/urokinase/ddg_results.csv @@ -0,0 +1,7 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +"10302 (1GJ7, no water pose)",11417 (no water pose),2.7104905347645314,0.042708112502457395,0.908488707688171,0.04281066752337177,0.25680000000000014,1.8020018270763605,0.06047095275683389,1.7009992333190098,0.03899561962350656 +"10302 (1GJ7, no water pose)",7806 (no water pose),-11.70297135446226,0.04813682201110126,-14.438869189258465,0.05212809236385452,2.1708999999999996,2.7358978347962055,0.07095415172365173,2.69913709994643,0.03650913442359283 +"10302 (1GJ7, no water pose)",8696 (no water pose),1.2982023972517442,0.04278242098949116,-1.4385128007184653,0.0453086146615028,1.0202299999999997,2.7367151979702093,0.06231537617848904,2.8723274166504815,0.03654612197436744 +11417 (no water pose),7806 (no water pose),-13.795112721179752,0.047088635184317114,-14.78012840029786,0.05167259900149545,1.9140999999999995,0.9850156791181084,0.06990992097757696,0.9981378666274203,0.037050439895690415 +11417 (no water pose),8696 (no water pose),-0.5788561766789283,0.04170801022890357,-1.857793202230734,0.0425582040813247,0.7634299999999996,1.2789370255518056,0.05958824424231685,1.1713281833314717,0.037086887594802824 +7806 (no water pose),8696 (no water pose),13.225886792591139,0.038338437161080964,13.038937702670987,0.038862195153425906,-1.1506699999999999,0.18694908992015247,0.054590346913141276,0.17319031670405138,0.03446296240906026 diff --git a/summaries/2026_june_08/water_set/urokinase/dg_comparison_plot.png b/summaries/2026_june_08/water_set/urokinase/dg_comparison_plot.png new file mode 100644 index 0000000..0b295dc Binary files /dev/null and b/summaries/2026_june_08/water_set/urokinase/dg_comparison_plot.png differ diff --git a/summaries/2026_june_08/water_set/urokinase/dg_plot.png b/summaries/2026_june_08/water_set/urokinase/dg_plot.png new file mode 100644 index 0000000..0f8703e Binary files /dev/null and b/summaries/2026_june_08/water_set/urokinase/dg_plot.png differ diff --git a/summaries/2026_june_08/water_set/urokinase/dg_results.csv b/summaries/2026_june_08/water_set/urokinase/dg_results.csv new file mode 100644 index 0000000..cb8e3cf --- /dev/null +++ b/summaries/2026_june_08/water_set/urokinase/dg_results.csv @@ -0,0 +1,5 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +"10302 (1GJ7, no water pose)",NC(=[NH2+])c1cc2cc(-c3cccc(-c4ccccc4)c3[O-])[nH]c2cc1Cl,-11.77853343747898,0.02721066105147956,-10.8224 +11417 (no water pose),NC(=[NH2+])c1cc2cc(-c3cccc(-c4ccccc4)c3[O-])[nH]c2cc1F,-10.07753420415997,0.027932745567929827,-10.5656 +7806 (no water pose),NC(=[NH2+])c1ccc2[nH]c(-c3cccc(-c4ccccc4)c3[O-])nc2c1,-9.07939633753255,0.0243412575990121,-8.6515 +8696 (no water pose),NC(=[NH2+])c1ccc2[nH]c(-c3cccc(-c4ccccc4)c3[O-])cc2c1,-8.906206020828499,0.02439669970522317,-9.80217