diff --git a/summaries/2026_apr_23/README.md b/summaries/2026_apr_23/README.md new file mode 100644 index 0000000..4ac9c55 --- /dev/null +++ b/summaries/2026_apr_23/README.md @@ -0,0 +1,14 @@ +# Summary +- Number of Datasets: 14 +- Number of Ligands: 353 +- Number of Edges: 607 +- Total Wallclock Time: 83.73 Hours +- Average Time Per Edge: 0.14 Hours +- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) + + +## Description +Results of switching to Reaction Field from the custom real space PME implementation inherited from Timemachine. + + +![Retrospective dG performance](dg_plot.png) diff --git a/summaries/2026_apr_23/dg_plot.png b/summaries/2026_apr_23/dg_plot.png new file mode 100644 index 0000000..157e992 Binary files /dev/null and b/summaries/2026_apr_23/dg_plot.png differ diff --git a/summaries/2026_apr_23/fragments/mcl1/README.md b/summaries/2026_apr_23/fragments/mcl1/README.md new file mode 100644 index 0000000..e1efe94 --- /dev/null +++ b/summaries/2026_apr_23/fragments/mcl1/README.md @@ -0,0 +1,40 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.66 +- RMSE: 0.86 +- R²: 0.24 +- Kendall 𝜏: 0.18 +- Spearman ρ: 0.27 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.57 Hours +- Average Time Per Edge: 0.08 Hours +- Total Nanoseconds Simulated: 2216.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/fragments/mcl1/ddg_results.csv b/summaries/2026_apr_23/fragments/mcl1/ddg_results.csv new file mode 100644 index 0000000..eef4217 --- /dev/null +++ b/summaries/2026_apr_23/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,-5.529757983783047,0.0640674841211962,-5.886120930104273,0.06337169613653576,-0.0600000000000005,0.35636294632122595,0.09011445163147334,0.481658755273048,0.07164441919664735 +10,15,-1.2133157260254024,0.06568631213721997,-1.0375669641561465,0.06396081478604689,-0.2699999999999996,-0.1757487618692558,0.09168248158881437,-0.3743346744192593,0.07502569737477952 +2,13 flipped,4.278683881330554,0.05685845065956202,1.9498584538842927,0.054886256326515344,0.1200000000000001,2.3288254274462616,0.07902774541226514,2.1531820879835424,0.055541983278263714 +2,14,1.7662506510772407,0.06545701428193855,2.1853887487247055,0.06643404229715566,-0.28000000000000025,-0.4191380976474647,0.09326361935206125,-0.17889513059760453,0.05903692160779348 +2,3,0.5677836340830087,0.045142028529103526,2.7891820674362204,0.04601330353612805,-1.0599999999999996,-2.2213984333532117,0.06445949768676645,-2.15291720133583,0.057303437544123086 +2,15,14.267290294936979,0.0717930537878102,15.270569875312216,0.07102531631443867,0.020000000000000462,-1.0032795803752377,0.10098929710491837,-0.8107734038494385,0.06444898719093037 +2,4,-4.857103470836736,0.04302544236044111,-4.630854888304673,0.04278723005697917,-0.47999999999999954,-0.22624858253206365,0.06067895637089107,-0.2301226672084491,0.05241313665341936 +2,5,0.6171208246742383,0.04514345392763493,0.44214222187786517,0.04361657429816907,-0.71,0.1749786027963732,0.0627721035653912,0.041790838036591005,0.05423435828160568 +3,4,-5.70477562707599,0.05244174576223522,-7.463287803622189,0.05381100455787853,0.5800000000000001,1.7585121765461984,0.0751382785943286,1.922794534127381,0.06464267667045868 +3,11,6.64138988759355,0.06290355904536601,5.048752579711695,0.06317268146352294,0.8399999999999999,1.5926373078818545,0.08914956771552839,1.4923633154651776,0.07022284986721485 +4,11,12.042659004660736,0.060989983229799434,12.68396810865816,0.06163746574565016,0.2599999999999998,-0.6413091039974244,0.08671190943531006,-0.43043121866220346,0.06629254545535411 +5,10,15.785400158513202,0.06263369574381074,15.943837455875455,0.06132286744850459,1.0,-0.15843729736225348,0.08765542718300515,-0.47822956746677026,0.06645712102440837 +5,8,12.34514632136168,0.05659750010868597,13.515650725321253,0.05778982270948334,-0.33000000000000007,-1.1705044039595722,0.08088844557380383,-1.1193406899953464,0.06150927270191533 +7,13 flipped,-11.063282657460709,0.05106685575240134,-12.254793279495312,0.05132247528723434,0.6699999999999999,1.191510622034602,0.07240041592453281,1.5391570931364775,0.05885229783312193 +7,14,-12.364697951117357,0.05573387607723207,-11.843163292956978,0.056548800030845746,0.2699999999999996,-0.521534658160378,0.07939793276604147,-0.7929201254446694,0.06216139611270257 +7,8,-1.8599247613999481,0.050555205819739886,-0.11435041533440979,0.05244786822225941,-0.4900000000000002,-1.7455743460655384,0.07284646674023217,-1.6915748468058203,0.05543330465485836 +7,9,-0.42064000466442114,0.054138352550401156,0.5252656635751675,0.054002723978191856,0.39999999999999947,-0.9459056682395885,0.07646734867861121,-1.141485238731108,0.06297815996433409 +8,10,2.740924236232082,0.05056681797190441,2.1917488649449584,0.05051527668713992,1.33,0.5491753712871236,0.07147584388156615,0.6411111225285762,0.06457053141982083 +9,13 flipped,-10.047883065185164,0.049782000224397174,-12.921753724567292,0.050797143544688415,0.27000000000000046,2.8738706593821277,0.07112381695776429,2.6806423318675856,0.06942862726655952 +9,15,0.35674210779718774,0.06068234114518923,0.6742916490008114,0.05937552552431238,0.17000000000000082,-0.31754954120362366,0.08489876063965479,-0.2833131599653953,0.07674043476272879 diff --git a/summaries/2026_apr_23/fragments/mcl1/dg_comparison_plot.png b/summaries/2026_apr_23/fragments/mcl1/dg_comparison_plot.png new file mode 100644 index 0000000..0cfce5e Binary files /dev/null and b/summaries/2026_apr_23/fragments/mcl1/dg_comparison_plot.png differ diff --git a/summaries/2026_apr_23/fragments/mcl1/dg_plot.png b/summaries/2026_apr_23/fragments/mcl1/dg_plot.png new file mode 100644 index 0000000..e6abb8a Binary files /dev/null and b/summaries/2026_apr_23/fragments/mcl1/dg_plot.png differ diff --git a/summaries/2026_apr_23/fragments/mcl1/dg_results.csv b/summaries/2026_apr_23/fragments/mcl1/dg_results.csv new file mode 100644 index 0000000..908f644 --- /dev/null +++ b/summaries/2026_apr_23/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,-6.056744453098339,0.05073102886450325,-5.55 +14,Cn1c(C(=O)[O-])cc2cc(Br)ccc21,-5.575085697825291,0.05058938141916612,-5.61 +10,Cc1ccc2c(C)c(C(=O)[O-])oc2c1C,-5.832629296657866,0.0490026113302768,-5.04 +15,Cc1cccc2c(-c3ccccc3)c(C(=O)[O-])[nH]c12,-6.206963971077125,0.05681196484355936,-5.31 +2,O=C([O-])c1sc2ccccc2c1Cl,-5.396190567227687,0.03043144098709231,-5.33 +13 flipped,Cn1c(C(=O)[O-])cc2ccccc21,-3.2430084792441445,0.046463311396542153,-5.21 +3,O=C([O-])c1sc2cccc(Cl)c2c1Cl,-7.549107768563517,0.04855524023030195,-6.39 +4,O=C([O-])c1sc2cc(Cl)ccc2c1Cl,-5.626313234436136,0.04267392990221465,-5.81 +5,Cc1ccc2c(Cl)c(C(=O)[O-])sc2c1,-5.354399729191096,0.04489201507692308,-6.04 +8,Cc1c(C(=O)[O-])oc2cc(Cl)ccc12,-6.473740419186442,0.04204875278354754,-6.37 +7,Cc1c(C(=O)[O-])oc2ccc(Cl)cc12,-4.782165572380622,0.036121373926062725,-5.88 +9,Cc1c(C(=O)[O-])oc2c(C)cccc12,-5.92365081111173,0.051589678988987794,-5.48 diff --git a/summaries/2026_apr_23/fragments/p38/README.md b/summaries/2026_apr_23/fragments/p38/README.md new file mode 100644 index 0000000..ece89e9 --- /dev/null +++ b/summaries/2026_apr_23/fragments/p38/README.md @@ -0,0 +1,40 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.01 +- RMSE: 1.18 +- R²: 0.80 +- Kendall 𝜏: 0.47 +- Spearman ρ: 0.71 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.62 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 1438.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/fragments/p38/ddg_results.csv b/summaries/2026_apr_23/fragments/p38/ddg_results.csv new file mode 100644 index 0000000..09d312e --- /dev/null +++ b/summaries/2026_apr_23/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,3,35.65161204417835,0.04625444606227205,34.826259534772014,0.04703411872698075,-0.1499999999999999,0.8253525094063343,0.06596728056355936,0.9410022384411483,0.048068692888810514 +1_1W7H,5_1WBW,7.959122016788604,0.06423178357627013,9.959157669388254,0.06306211822239018,-2.0000000000000004,-2.0000356525996508,0.09001418097213083,-2.206755955167331,0.05694248966414323 +1_1W7H,6,5.321509944827347,0.07051716541002628,8.274987461101535,0.07196113367323605,-1.1,-2.9534775162741873,0.10075254526314635,-2.9642669267119293,0.05858912225565009 +4,3,38.3708634841859,0.06105890944375494,35.05070393460433,0.058894324940924336,1.3100000000000005,3.3201595495815672,0.08483355428548216,3.310460134549574,0.05144833699002701 +4,5_1WBW,10.375428814136653,0.06441129388177416,10.133045260848018,0.06459735229035656,-0.54,0.24238355328863515,0.09122298341124736,0.16270194094109502,0.059822899228904464 +4,7,9.601137864842634,0.07131624781141219,12.133188208287079,0.072266307467302,-0.8999999999999995,-2.5320503434444452,0.1015304210414661,-2.419451497942438,0.06632312191049836 +5_1WBW,3,28.53281748299989,0.06793084000926687,25.051324543581018,0.06997645920065128,1.8500000000000005,3.4814929394188705,0.09752591382102002,3.147758193608479,0.05523490382943601 +6,3,30.09464669349634,0.06841660094122753,26.499773396445338,0.06709043398831095,0.9500000000000002,3.594873297051003,0.09582253188624837,3.9052691651530775,0.05693094693208166 +6,7,2.0578751297870466,0.075261258369717,3.4723236552127186,0.07810239890546916,-1.2599999999999998,-1.4144485254256722,0.10846308923399853,-1.8246424673389345,0.07066086497842312 +7,3,29.152292375822885,0.07393697153690112,23.170254101799017,0.0711532720845785,2.21,5.982038274023866,0.10261317599797107,5.729911632492012,0.0622163308854694 diff --git a/summaries/2026_apr_23/fragments/p38/dg_comparison_plot.png b/summaries/2026_apr_23/fragments/p38/dg_comparison_plot.png new file mode 100644 index 0000000..5d0f6bb Binary files /dev/null and b/summaries/2026_apr_23/fragments/p38/dg_comparison_plot.png differ diff --git a/summaries/2026_apr_23/fragments/p38/dg_plot.png b/summaries/2026_apr_23/fragments/p38/dg_plot.png new file mode 100644 index 0000000..50f2437 Binary files /dev/null and b/summaries/2026_apr_23/fragments/p38/dg_plot.png differ diff --git a/summaries/2026_apr_23/fragments/p38/dg_results.csv b/summaries/2026_apr_23/fragments/p38/dg_results.csv new file mode 100644 index 0000000..c68b920 --- /dev/null +++ b/summaries/2026_apr_23/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,-3.2202686777337663,0.03537055105693716,-3.94 +3,c1ccc(COc2cccnc2)cc1,-2.279266439292618,0.032550320335864344,-4.09 +5_1WBW,Nc1ncccc1OCc1cccc2ccccc12,-5.427024632901097,0.04462478287991618,-5.94 +6,OCCNc1ccc(OCc2c(Cl)cccc2Cl)cn1,-6.184535604445696,0.04670770134160013,-5.04 +4,Nc1ncccc1OCc1c(Cl)cccc1Cl,-5.589726573842192,0.03984228940550477,-5.4 +7,CC(C)(CO)Nc1ccc(OCc2c(Cl)cccc2Cl)cn1,-8.00917807178463,0.05302215079457669,-6.3 diff --git a/summaries/2026_apr_23/jacs_set/jnk1/README.md b/summaries/2026_apr_23/jacs_set/jnk1/README.md new file mode 100644 index 0000000..7888c29 --- /dev/null +++ b/summaries/2026_apr_23/jacs_set/jnk1/README.md @@ -0,0 +1,40 @@ +# Jnk1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.24 +- RMSE: 1.36 +- R²: 0.55 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.75 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.46 Hours +- Average Time Per Edge: 0.10 Hours +- Total Nanoseconds Simulated: 3701.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/jacs_set/jnk1/ddg_results.csv b/summaries/2026_apr_23/jacs_set/jnk1/ddg_results.csv new file mode 100644 index 0000000..7cd44e6 --- /dev/null +++ b/summaries/2026_apr_23/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,-4.9177503280793555,0.05668730250657119,-7.319395260017533,0.05687405027963815,0.2699999999999996,2.4016449319381774,0.08030011121214167,2.461034547153657,0.06336013622209431 +17124-1,18637-1,-15.762959216837675,0.060642039509216546,-14.924542850514399,0.06084770529903959,-0.46000000000000085,-0.8384163663232774,0.08590634549319481,-0.7053057371278282,0.07673558275179086 +17124-1,18652-1,-20.619431270736204,0.06210567515519432,-19.207861472366616,0.05824669289357324,-1.0,-1.4115697983695872,0.08514571110467489,-1.6266961024647468,0.07690906720064457 +17124-1,18660-1,-41.20824832423885,0.06596426283142492,-41.13399883202469,0.06594427396531281,0.9800000000000004,-0.07424949221416807,0.09327342193629191,-0.05314228010811206,0.07820415031344975 +18626-1,18628-1_flip,0.8474003180469143,0.05209537978401186,0.023923831283292625,0.05234494367036383,0.16999999999999993,0.8234764867636217,0.07385067178227965,0.9268386007150919,0.07154796778986475 +18626-1,18632-1,2.726164658187396,0.047680129348116544,2.905777332064504,0.049277385364961054,-0.21000000000000085,-0.17961267387710794,0.06856861850044817,-0.19335319811462615,0.06726097682161691 +18626-1,18635-1,1.0548238556477618,0.05008504972803464,0.5372144280807579,0.04944037238193507,1.5799999999999992,0.517609427567004,0.07037657726491188,0.4382180090970689,0.07221596912024805 +18627-1,18625-1,-3.6534998076324334,0.0539684087996401,-3.040963170296715,0.05245705589106945,0.370000000000001,-0.6125366373357183,0.07526175563407922,-0.2752706796640254,0.07294685158328118 +18627-1,18630-1,1.136825972923424,0.03838836846896734,0.9493839143853757,0.03597882999681667,-0.6600000000000001,0.18744205853804838,0.05261314514120061,0.0031985592144065933,0.06747079395237006 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b/summaries/2026_apr_23/jacs_set/jnk1/dg_results.csv new file mode 100644 index 0000000..0be5da6 --- /dev/null +++ b/summaries/2026_apr_23/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,-10.883482571331077,0.05159972184607094,-9.68 +18631-1,CCOc1nc(NC(=O)Cc2ccccc2OC)cc(N)c1C#N,-8.42244802417742,0.036769220381869104,-9.41 +18637-1,CCOc1nc(NC(=O)Cc2cc(OC)c(NC(C)=O)cc2OC)cc(N)c1C#N,-11.588788308458906,0.056796288308876786,-10.14 +18652-1,COc1cc(S(C)(=O)=O)c(OC)cc1CC(=O)Nc1cc(N)c(C#N)c(OC(C)C)n1,-12.510178673795824,0.05703045960783913,-10.68 +18660-1,COc1ccc(OC)c(CC(=O)Nc2cc(N)c(C#N)c(OCCS(C)(=O)=O)n2)c1,-10.93662485143919,0.05876527743197297,-8.7 +18626-1,CCOc1nc(NC(=O)Cc2cccc(Cl)c2)cc(N)c1C#N,-7.7454157782331166,0.0523906725642038,-8.87 +18628-1_flip,CCOc1nc(NC(=O)Cc2ccccc2C)cc(N)c1C#N,-6.818577177518025,0.048727088186448275,-8.7 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+18658-1,COc1ccc(OC)c(CC(=O)Nc2cc(N)c(C#N)c(OCCO)n2)c1,-9.80231385112578,0.04920451627735379,-9.7 +18638-1,CCOc1nc(NC(=O)Cc2cc(OC)c(S(C)(=O)=O)cc2OC)cc(N)c1C#N,-11.478888264402123,0.0593334634925601,-10.09 +18639-1,CCOc1nc(NC(=O)Cc2cc(OC)c([N+](=O)[O-])cc2OC)cc(N)c1C#N,-11.500705178092359,0.06500012514851265,-9.74 +18659-1,COCCOc1nc(NC(=O)Cc2cc(OC)ccc2OC)cc(N)c1C#N,-10.858163839127528,0.053693439546188874,-9.47 diff --git a/summaries/2026_apr_23/jacs_set/mcl1/README.md b/summaries/2026_apr_23/jacs_set/mcl1/README.md new file mode 100644 index 0000000..721127c --- /dev/null +++ b/summaries/2026_apr_23/jacs_set/mcl1/README.md @@ -0,0 +1,40 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.22 +- RMSE: 1.67 +- R²: 0.44 +- Kendall 𝜏: 0.48 +- Spearman ρ: 0.65 + +## System Details +- Ligands: 42 +- Host Atoms: 2542 +- Map Details: + - Edges: 73 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.82 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 8141.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/jacs_set/mcl1/ddg_results.csv b/summaries/2026_apr_23/jacs_set/mcl1/ddg_results.csv new file mode 100644 index 0000000..387038a --- /dev/null +++ b/summaries/2026_apr_23/jacs_set/mcl1/ddg_results.csv @@ -0,0 +1,74 @@ +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,-0.48277010240537577,0.06410564913222246,-0.7623288690004307,0.06264930781464495,0.16000000000000014,0.279558766595055,0.0896352052506031,0.44780984801428225,0.08029796071631923 +23,51,6.347242610361088,0.06330811544866585,4.274260813850864,0.06379647969545853,0.3800000000000008,2.072981796510225,0.08987718455311479,2.204408163751154,0.09792692260105351 +23,54,-0.9449383402224327,0.06169710659865794,-0.36178543681895664,0.061762254392338053,-0.9499999999999993,-0.583152903403476,0.08729896351200306,-0.7710995570594843,0.09557856051536907 +23,57,13.864291574992642,0.05677557582911138,13.937116399882957,0.058190671014201216,-0.20999999999999908,-0.07282482489031455,0.08129957074800687,-0.06101414932714988,0.09049946584360423 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a/summaries/2026_apr_23/jacs_set/mcl1/dg_plot.png b/summaries/2026_apr_23/jacs_set/mcl1/dg_plot.png new file mode 100644 index 0000000..27cd223 Binary files /dev/null and b/summaries/2026_apr_23/jacs_set/mcl1/dg_plot.png differ diff --git a/summaries/2026_apr_23/jacs_set/mcl1/dg_results.csv b/summaries/2026_apr_23/jacs_set/mcl1/dg_results.csv new file mode 100644 index 0000000..7d2ff45 --- /dev/null +++ b/summaries/2026_apr_23/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,-8.716620338283052,0.05947636892728151,-8.83 +44,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-8.26881049026877,0.05394741916371392,-8.67 +51,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-6.512212174531898,0.07779616770341986,-8.45 +54,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-9.487719895342536,0.07481859908749942,-9.78 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-0,0 +1,40 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.33 +- RMSE: 1.60 +- R²: 0.45 +- Kendall 𝜏: 0.49 +- 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 7.96 Hours +- Average Time Per Edge: 0.13 Hours +- Total Nanoseconds Simulated: 7799.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - 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a/summaries/2026_apr_23/jacs_set/ptp1b/README.md b/summaries/2026_apr_23/jacs_set/ptp1b/README.md new file mode 100644 index 0000000..c474788 --- /dev/null +++ b/summaries/2026_apr_23/jacs_set/ptp1b/README.md @@ -0,0 +1,40 @@ +# Ptp1B Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.19 +- RMSE: 2.05 +- R²: 0.31 +- Kendall 𝜏: 0.58 +- Spearman ρ: 0.69 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.40 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 5553.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/jacs_set/ptp1b/ddg_results.csv b/summaries/2026_apr_23/jacs_set/ptp1b/ddg_results.csv new file mode 100644 index 0000000..bc29c8b --- /dev/null +++ b/summaries/2026_apr_23/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) +20667,23485,7.329116895547587,0.044696560646385,4.944878702519934,0.0436368717902162,0.41000000000000014,2.384238193027653,0.062465663474037786,2.6746365410523936,0.11043463718033372 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--git a/summaries/2026_apr_23/jacs_set/ptp1b/dg_plot.png b/summaries/2026_apr_23/jacs_set/ptp1b/dg_plot.png new file mode 100644 index 0000000..f205f02 Binary files /dev/null and b/summaries/2026_apr_23/jacs_set/ptp1b/dg_plot.png differ diff --git a/summaries/2026_apr_23/jacs_set/ptp1b/dg_results.csv b/summaries/2026_apr_23/jacs_set/ptp1b/dg_results.csv new file mode 100644 index 0000000..693dce7 --- /dev/null +++ b/summaries/2026_apr_23/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,-12.788286081990943,0.07493462198446203,-11.42 +23485,Cc1c(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc(C(=O)[O-])c1OCC(=O)[O-],-10.11364954093855,0.08112096841876167,-11.01 +23482,CS(=O)(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-10.622696876061863,0.05511920889507726,-10.01 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+23480,COC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-9.294702014456087,0.0693842148246561,-8.72 +23484,O=C([O-])COc1cc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc1C(=O)[O-],-16.322139410580547,0.07188626032372757,-7.75 diff --git a/summaries/2026_apr_23/merck/cdk8/README.md b/summaries/2026_apr_23/merck/cdk8/README.md new file mode 100644 index 0000000..cc3282d --- /dev/null +++ b/summaries/2026_apr_23/merck/cdk8/README.md @@ -0,0 +1,40 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.79 +- RMSE: 2.14 +- R²: 0.70 +- Kendall 𝜏: 0.63 +- Spearman ρ: 0.80 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 20.08 Hours +- Average Time Per Edge: 0.35 Hours +- Total Nanoseconds Simulated: 8489.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/cdk8/ddg_results.csv b/summaries/2026_apr_23/merck/cdk8/ddg_results.csv new file mode 100644 index 0000000..62f7f89 --- /dev/null +++ b/summaries/2026_apr_23/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) 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@@ +# Eg5 Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.18 +- RMSE: 1.43 +- R²: 0.58 +- 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.84 Hours +- Average Time Per Edge: 0.12 Hours +- Total Nanoseconds Simulated: 1845.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/eg5_neutral/ddg_results.csv b/summaries/2026_apr_23/merck/eg5_neutral/ddg_results.csv new file mode 100644 index 0000000..6ee8fff --- /dev/null +++ b/summaries/2026_apr_23/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,CHEMBL1078998,11.498754858101195,0.0628575829617732,7.5037118107579035,0.06193111379916761,-0.18320000000000114,3.995043047343292,0.08824136553908064,2.9830100784902296,0.06398173474071465 +CHEMBL1078691,CHEMBL1084115,5.421670129943012,0.06129453896940952,2.984017304415389,0.06092879319977463,0.7516800000000003,2.4376528255276226,0.0864253339493309,2.6363952847809937,0.06439235708320547 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@@ +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,-12.567868725299265,0.0406444709042601,-10.2494 +CHEMBL1078998,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1cccs1)N2,-9.584858646809035,0.04941345328292617,-10.4326 +CHEMBL1084115,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccsc1)N2,-9.931473440518271,0.049943994990827426,-9.49772 +CHEMBL1078774,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)c(F)c1)N2,-12.84139587749516,0.04068853663719933,-10.6625 +CHEMBL1089056,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-9.573212951561535,0.0291004288362956,-9.49772 +CHEMBL1085895,O=C(NCCCO)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.23519581483308,0.05408766031850971,-10.9219 +CHEMBL1088740,Cc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-6.575938157797889,0.03048764737878962,-8.75107 +CHEMBL1093088,FC(F)(F)c1ccc2c(c1)[C@H]1O[C@@H](Cn3cncn3)CC[C@H]1[C@H](c1ccccc1)N2,-10.209628533476206,0.05166474710542041,-11.2832 +CHEMBL1089393,Clc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-7.206367852209559,0.04354357975576184,-8.42983 diff --git a/summaries/2026_apr_23/merck/eg5_positive_1/README.md b/summaries/2026_apr_23/merck/eg5_positive_1/README.md new file mode 100644 index 0000000..ba0ce52 --- /dev/null +++ b/summaries/2026_apr_23/merck/eg5_positive_1/README.md @@ -0,0 +1,40 @@ +# Eg5 Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.18 +- RMSE: 1.36 +- R²: 0.22 +- Kendall 𝜏: 0.26 +- Spearman ρ: 0.42 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.12 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 5070.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/eg5_positive_1/ddg_results.csv b/summaries/2026_apr_23/merck/eg5_positive_1/ddg_results.csv new file mode 100644 index 0000000..a7f19dc --- /dev/null +++ b/summaries/2026_apr_23/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,CHEMBL1084676,10.53227435346999,0.06226011190178522,10.950010495773501,0.061326205415072665,0.3335000000000008,-0.41773614230351025,0.08739121812078433,-0.5263243303001612,0.11704770304640634 +CHEMBL1077204,CHEMBL1085692,29.203903040305452,0.07844817084977264,28.2207855052993,0.07870272121927865,-0.2800999999999991,0.9831175350061516,0.11112260722730821,0.5996356340614497,0.10683091619110799 +CHEMBL1077227,CHEMBL1084935,18.843401192619787,0.07865090652871604,18.433718041463184,0.07834871251142375,0.7956000000000003,0.40968315115660153,0.1110157009165215,0.5811601182252186,0.09882281208670886 +CHEMBL1077227,CHEMBL1086410,1.932796190215743,0.05804407460450977,1.6778300443744778,0.057806509865081054,-0.1330000000000009,0.254966145841265,0.08191890611742571,0.10180017053624901,0.09992224505683053 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a/summaries/2026_apr_23/merck/eg5_positive_1/dg_results.csv b/summaries/2026_apr_23/merck/eg5_positive_1/dg_results.csv new file mode 100644 index 0000000..d9f3e7a --- /dev/null +++ b/summaries/2026_apr_23/merck/eg5_positive_1/dg_results.csv @@ -0,0 +1,20 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1077204,C[NH+](C)CCNC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.010156495389133,0.08135729029645812,-11.1117 +CHEMBL1084676,C[NH+](C)CCOC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.536480825689294,0.08414960548961332,-10.7782 +CHEMBL1085692,C[NH+](C)CCCC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-10.410520861327683,0.06923753295611694,-11.3918 +CHEMBL1077227,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1cccs1,-9.74228043469704,0.06868006501201535,-11.3918 +CHEMBL1084935,CC[N@H+](CCO)C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-9.161120316471822,0.07105629358945142,-10.5962 +CHEMBL1086410,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-9.640480264160791,0.07257757041361085,-11.5248 +CHEMBL1082248,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-10.15565478147398,0.05396907247523709,-11.6963 +CHEMBL1083517,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccc(O)cc1,-13.971485704708677,0.061633228119587075,-11.5248 +CHEMBL1096002,OCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Cl)cc(F)c1N[C@H]2c1ccccc1,-10.623522769389009,0.0526124420355558,-11.1913 +CHEMBL1082249,CC(=O)NCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-10.201957405571797,0.0661865379663185,-11.2832 +CHEMBL1083836,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C3CC3)ccc1N[C@H]2c1ccccc1,-10.660642207934377,0.0674139863523505,-10.9219 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+CHEMBL1093087,[NH3+]CCN(C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1)c1ccccc1,-10.020668102302277,0.07975894191405898,-10.5962 diff --git a/summaries/2026_apr_23/merck/hif2a/README.md b/summaries/2026_apr_23/merck/hif2a/README.md new file mode 100644 index 0000000..de78c2f --- /dev/null +++ b/summaries/2026_apr_23/merck/hif2a/README.md @@ -0,0 +1,40 @@ +# Hif2A Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.80 +- RMSE: 2.08 +- R²: 0.15 +- Kendall 𝜏: 0.21 +- Spearman ρ: 0.30 + +## System Details +- Ligands: 41 +- Host 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.01 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 7835.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/hif2a/ddg_results.csv b/summaries/2026_apr_23/merck/hif2a/ddg_results.csv new file mode 100644 index 0000000..1236328 --- /dev/null +++ b/summaries/2026_apr_23/merck/hif2a/ddg_results.csv @@ -0,0 +1,71 @@ +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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[3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.96 Hours +- Average Time Per Edge: 0.08 Hours +- Total Nanoseconds Simulated: 6552.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/hif2a_jmc2023/ddg_results.csv b/summaries/2026_apr_23/merck/hif2a_jmc2023/ddg_results.csv new file mode 100644 index 0000000..b8e7620 --- /dev/null +++ b/summaries/2026_apr_23/merck/hif2a_jmc2023/ddg_results.csv @@ -0,0 +1,63 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg 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+35n,CS(=O)(=O)c1sc(OCC2CC(F)(F)C2)c2c1[C@H](O)C(F)(F)C2,-10.681996902508814,0.0830077593263935,-9.74957000407174 +35m,CC(F)(F)COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-11.79547949683989,0.05186382975076697,-9.658749832281092 +35s,CC(F)(F)CCOc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-8.74965649884395,0.061038303133755405,-9.258622958144626 diff --git a/summaries/2026_apr_23/merck/pfkfb3/README.md b/summaries/2026_apr_23/merck/pfkfb3/README.md new file mode 100644 index 0000000..43e9c8d --- /dev/null +++ b/summaries/2026_apr_23/merck/pfkfb3/README.md @@ -0,0 +1,40 @@ +# Pfkfb3 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.04 +- RMSE: 1.29 +- R²: 0.36 +- Kendall 𝜏: 0.46 +- Spearman ρ: 0.63 + +## System Details +- Ligands: 40 +- Host Atoms: 8158 +- Map Details: + - Edges: 71 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 10.03 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 7754.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/pfkfb3/ddg_results.csv b/summaries/2026_apr_23/merck/pfkfb3/ddg_results.csv new file mode 100644 index 0000000..d940cdb --- /dev/null +++ b/summaries/2026_apr_23/merck/pfkfb3/ddg_results.csv @@ -0,0 +1,72 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err 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mode 100644 index 0000000..cfd0ece --- /dev/null +++ b/summaries/2026_apr_23/merck/pfkfb3/dg_results.csv @@ -0,0 +1,41 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +19,Cn1ccc2ccc(-c3cc(Nc4ccccc4)cc4nccnc34)cc21,-7.908730346466913,0.07419239669406989,-7.55079 +23,Cn1ccc2ccc(-c3cc(Nc4cccnc4)cc4nccnc34)cc21,-8.621681205166173,0.07484584340708475,-7.914460000000001 +33,Cn1ccc2ccc(-c3cc(Nc4cnccc4C#N)cc4nccnc34)cc21,-9.282877356683905,0.06495793799016643,-8.60692 +20,COc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-7.544902382623649,0.0936993989213423,-8.51645 +42,CSc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-7.463936962720455,0.08877405110155816,-8.4668 +24,Cn1ccc2ccc(-c3cc(Nc4ccccc4C#N)cc4nccnc34)cc21,-8.669064832556726,0.0738276877403673,-8.86991 +29,Cn1ccc2ccc(-c3cc(Nc4ccccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.325189040058014,0.047424052257958024,-9.64602 +26,Cn1ccc2ccc(-c3cc(Nc4ccccc4C(N)=O)cc4nccnc34)cc21,-8.454462340919559,0.07121699570412855,-9.16944 +37,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(=O)NC4CCOCC4)cc4nccnc34)cc21,-10.839154897771161,0.08692164077028655,-9.99707 +36,CN(c1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1)c1cnccc1S(C)(=O)=O,-10.39318613948252,0.052940036515725306,-7.44054 +55,Cn1ccc2c(F)cc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-10.708584811869562,0.04824491642556341,-10.6355 +57,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ccn(C(F)F)c3c2)c2nccnc2c1,-10.913422308240472,0.06417332553583606,-10.4744 +60_adjust,CC1(C)COc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-10.237134298106232,0.06397545476594461,-8.14374 +30_flip_b,COc1ncccc1Nc1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1,-7.454853637420261,0.07402371449902037,-9.19819 +31,COc1ccncc1Nc1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1,-10.564494343607707,0.07475647609574536,-9.28247 +34,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(N)=O)cc4nccnc34)cc21,-9.598798230859805,0.08347609727448976,-9.97238 +35,Cn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-10.494268635423223,0.044620474608548816,-10.1388 +52,CCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.821132627373526,0.05707930047327606,-10.3953 +53,CCCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.607092272486685,0.06276129187509479,-6.99764 +70,Cc1coc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-11.27833610029899,0.05604376086696667,-10.3039 +38,CN(C)c1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-10.260086657927609,0.06467156678420351,-8.75876 +69,Cc1csc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-11.6139165886779,0.03758269603913295,-10.7146 +41,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(OC(F)(F)F)c2)c2nccnc2c1,-8.017039772147157,0.0944588456589849,-7.38769 +43,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(Br)c2)c2nccnc2c1,-7.735970866923139,0.08323616577576297,-7.997660000000001 +44,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(Br)cc2)c2nccnc2c1,-7.274043387829426,0.0628955902332619,-9.94868 +46,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(C(F)(F)F)cc2)c2nccnc2c1,-6.180621262161056,0.06226926459335439,-7.859360000000001 +63,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nsnc3c2)c2nccnc2c1,-8.229138344098581,0.05938372396197531,-8.56164 +47,CCc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.032779263665567,0.07605065729895993,-8.33345 +64,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ncsc3c2)c2nccnc2c1,-7.927304329092643,0.06228934523800877,-9.42228 +48,COc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.986749578084635,0.06966859709780683,-8.00636 +49,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(N)cc2)c2nccnc2c1,-5.157501292977699,0.07912632738635905,-7.93429 +62_flip,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nonc3c2)c2nccnc2c1,-6.808038479972596,0.07928201867820155,-7.691739999999999 +54,CC(C)n1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.840364024993475,0.06781911192202073,-8.17959 +56,Cc1cc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc2c1ccn2C,-11.121019309456905,0.05119842247525205,-10.5657 +58,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)CCO3)c2nccnc2c1,-9.370984536377662,0.07020902723626037,-9.13315 +39,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(N)c2)c2nccnc2c1,-7.2804193143878875,0.05675002730021153,-7.1975 +59,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)OCCO3)c2nccnc2c1,-9.342437622271984,0.07802828529815556,-8.11517 +65,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3scnc3c2)c2nccnc2c1,-9.080608488109704,0.04789989173807898,-9.4879 +67,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)nc3c2)c2nccnc2c1,-11.237345081331119,0.0583940246978511,-10.2436 +68,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)cc3c2)c2nccnc2c1,-10.360399029377707,0.05808758265029864,-9.77823 diff --git a/summaries/2026_apr_23/merck/shp2/README.md b/summaries/2026_apr_23/merck/shp2/README.md new file mode 100644 index 0000000..8cbdb47 --- /dev/null +++ b/summaries/2026_apr_23/merck/shp2/README.md @@ -0,0 +1,40 @@ +# Shp2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.56 +- RMSE: 2.09 +- R²: 0.15 +- Kendall 𝜏: 0.26 +- Spearman ρ: 0.34 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 7.35 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 5593.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/merck/shp2/ddg_results.csv b/summaries/2026_apr_23/merck/shp2/ddg_results.csv new file mode 100644 index 0000000..2ad7d16 --- /dev/null +++ b/summaries/2026_apr_23/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,-58.314200046635825,0.05103761181174604,-55.712440307799184,0.052383091785992646,-2.00282,-2.6017597388366367,0.0731356693037413,-2.5101614643319916,0.060604017603598535 +10,Example 23,-16.810406593499025,0.05577555758699442,-15.82453208016987,0.0576013183054181,-1.5860599999999998,-0.9858745133291548,0.08017995194973757,-0.5624087728896967,0.06983899838118748 +11,10,7.0087684373468395,0.05551388893900779,8.879756793325058,0.054044731480073493,-0.8001899999999997,-1.8709883559782186,0.07747660850789571,-1.37280179642873,0.06205982489649859 +11,Example 30,-50.287634713988155,0.052273368631516125,-46.665543484553844,0.05417980272193575,-2.8030099999999996,-3.622091229434307,0.07528582928462867,-3.8829632607607216,0.05599379124686614 +3,6,-10.908234530005037,0.07367688660864934,-12.252989038689885,0.0712164103871959,-2.5671,1.3447545086848476,0.1024698039852779,0.7692160027210804,0.0979469252413725 +3,Example 27,91.02554434336463,0.05520808883685243,90.40195609718663,0.05578078362373484,-3.0555900000000005,0.6235882461780035,0.07848202911938322,0.5570173774506078,0.11512541101757968 +4,3,0.8279980791810344,0.04330961283788846,0.23483407335866371,0.04274634121346797,0.3591300000000004,0.5931640058223707,0.0608520521536129,0.38345005807920884,0.1125211679421958 +4,SHP836-2,-0.6135603670329594,0.05271457079636308,-1.517259374156851,0.05022646481195546,-0.89114,0.9036990071238916,0.07281156324205226,1.2211156849521405,0.1093717898916364 +4,Example 27,91.64608462864057,0.05922568516787709,90.68283465659412,0.059385389456471614,-2.69646,0.9632499720464465,0.08387077121680298,0.9404674355298166,0.11570783655043432 +7,6,-32.74040796034972,0.057382847850221234,-33.13280874082966,0.05410918899806435,-0.95357,0.3924007804799375,0.07887075225601622,-0.04956299707963652,0.0860332991506746 +Example 14,6,-76.44497638301317,0.08003404402597893,-83.15651630610702,0.08146452968430884,1.748190000000001,6.711539923093851,0.11420121628002904,5.929238109750635,0.09653936685679869 +Example 14,Example 27,20.560554990730335,0.0825065957909275,15.030346725790203,0.0805813068748052,1.2597000000000005,5.530208264940131,0.11532859734974248,5.717039484480162,0.11393028329131465 +Example 14,Example 9,-2.9780372238103134,0.08174853245076147,-0.8455222591678785,0.07982669119058786,0.9841300000000004,-2.132514964642435,0.11425901795609254,-1.5328029071343714,0.0979358144584919 +Example 1,6,-9.223036113005918,0.05885137482610963,-9.367646265679342,0.05769724717538538,0.9581400000000002,0.14461015267342486,0.08241636154636267,0.9392282734487463,0.07012565655494914 +Example 1,7,25.59560106794795,0.06940932013720569,23.967083442645112,0.06751675959906063,1.9117100000000002,1.628517625302836,0.096830607499212,0.9887912705283828,0.07522437104685283 +Example 1,Example 3,-6.0599912487590615,0.06843176309423413,-5.730687999080884,0.06551939976068016,0.7723099999999992,-0.32930324967817703,0.09474016014967042,-0.25084950944768636,0.06946167963644666 +Example 1,Example 4,-5.890994178931669,0.06852081147963651,-5.418092680024372,0.06499290802584866,0.7870899999999992,-0.47290149890729677,0.09444140881776546,-0.28116135629468175,0.07352437791927555 +Example 1,Example 5,5.408152486091686,0.052466882552375776,3.205532982998232,0.04991047322511143,1.42509,2.2026195030934543,0.07241428797080973,1.9856800520381999,0.06530221298609146 +Example 1,Example 8,74.79214434601798,0.06318480524096136,80.4493085477932,0.0631066341549287,-0.7241499999999998,-5.657164201775218,0.08930155030962358,-5.872855951341235,0.06044639370730257 +Example 22,Example 24,-1.7010802350631316,0.04513550149716827,-2.816763249511607,0.04704065773398943,0.1616099999999996,1.1156830144484753,0.0651923076401443,0.9785722675132309,0.08857144275792195 +Example 22,Example 26,4.0553818583824714,0.05572624589358225,2.909380177875048,0.05405598404442268,0.2797800000000006,1.1460016805074231,0.07763674318518823,0.8914234592584842,0.08842399963551621 +Example 22,Example 6,-96.12308422990266,0.06254694504934767,-96.55262316404304,0.060292468204259715,0.16957000000000022,0.429538934140381,0.08687520968128817,0.9917936617840137,0.08563989448831902 +Example 24,Example 23,2.583373995637663,0.042084967202749075,4.385535141772099,0.04209018392077691,0.33688000000000073,-1.8021611461344358,0.05952082028115281,-1.7851889186219712,0.08095433643918028 +Example 24,Example 25,8.767882799746667,0.0402892241577881,7.416469111167069,0.04163714681488027,0.20730999999999966,1.3514136885795982,0.05793853275774586,1.2270354944924025,0.08803677261700843 +Example 25,Example 23,-5.847145821186227,0.04859437103358848,-3.1003854880898247,0.04874106215884451,0.12957000000000107,-2.746760333096402,0.0688266230213455,-3.0122244131143736,0.0810115792748305 +Example 26,Example 23,-2.8703547406525796,0.04947173961222419,-1.2887625923919552,0.05060937565076925,0.21870999999999974,-1.581592148260624,0.07077260715856373,-1.6980401103672245,0.08079299367909272 +Example 26,Example 25,0.5536697192070335,0.06125266587234622,-0.8989325098557268,0.05948152569729869,0.08913999999999866,1.45260222906276,0.08538115117370866,1.3141843027471491,0.08788843252749914 +Example 29,Example 28,9.808400704373781,0.07578183906140325,10.798031102776498,0.07699568777298654,-0.8345700000000003,-0.9896303984027175,0.10803343495031366,-1.2224477195760235,0.10188044269711265 +Example 29,Example 30,-45.104125472705874,0.0713720522159105,-41.99676344290082,0.07087361332913444,-1.5343200000000001,-3.1073620298050533,0.10058349220343425,-2.5987959234028013,0.07955195574662119 +Example 2,Example 1,-1.8581971360294505,0.03894809078751742,-0.44001594136335476,0.03573304815624637,-0.7119599999999995,-1.4181811946660958,0.05285645189122442,-1.3886300672795056,0.06179987554404959 +Example 2,Example 30,48.6827564404107,0.04846834244937573,52.4582217265673,0.045453614765857846,-0.8808799999999994,-3.775465286156597,0.06644705648163031,-3.7922853885089776,0.0609122066269277 +Example 2,Example 4,-7.134601522664589,0.07429436723929529,-5.538985276793521,0.0737588032529631,0.0751299999999997,-1.5956162458710677,0.10469008578082545,-1.6697914235741873,0.07778479042697659 +Example 30,Example 23,41.59827027079817,0.048967686259901576,39.69294985295403,0.050203284525951075,0.41676,1.905320417844135,0.07012990856148148,1.947752691442295,0.0645086698584079 +Example 30,Example 3,-56.276742640590356,0.06865555193659272,-58.65005758457342,0.0684223573825697,0.9412299999999991,2.3733149439830563,0.09692885948728723,2.1528058117817856,0.06867311873519263 +Example 30,Example 5,-45.61119750105008,0.05855894475199314,-49.79024888530759,0.05532597741563088,1.59401,4.179051384257512,0.0805612424647354,4.389335373267672,0.06446279019544816 +Example 4,Example 3,-0.548473650613934,0.03574829386571356,-0.5422065474645374,0.0347189348308316,-0.014780000000000015,-0.006267103149396604,0.049833171182425716,0.030311846846995394,0.08400103536519653 +Example 6,Example 5,9.212346959353761,0.045715571124619186,8.603658604793837,0.041887458261098014,1.50617,0.6086883545599239,0.06200381119596879,0.643172368932623,0.07769799532124277 +Example 6,Example 28,114.37949805102836,0.07708004772841617,117.52069132788586,0.0763574605465198,0.61191,-3.1411932768574924,0.10849790568913413,-2.369814800508271,0.09428344414538331 +Example 9,7,-45.28208264292018,0.06591922751704692,-52.817998158069,0.06540145005822406,1.7176300000000007,7.535915515148824,0.09285846340621069,7.511604013964643,0.08759739130411394 +Example 9,Example 8,5.026894961243769,0.05039148532143123,4.628162908299583,0.05112094112099338,-0.9182299999999994,0.3987320529441864,0.07178197833715709,0.6499567920950255,0.075288534825096 +SHP099-1 Example 7,11,14.981213539500057,0.05027222583371222,12.366063050959966,0.049531250619989996,3.398559999999999,2.615150488540092,0.07057365994658363,2.799279912353885,0.06507859593578638 +SHP099-1 Example 7,Example 28,20.975439645745887,0.0736492802195641,20.205259383984284,0.07107936514737956,1.2952999999999992,0.7701802617616049,0.10235473915073201,0.29266485541994136,0.09004309897784418 +SHP099-1 Example 7,Example 29,9.0866598947562,0.06935184841447312,7.853508500396704,0.06700552963569126,2.1298699999999995,1.2331513943594958,0.09643349978230364,1.5151125749959649,0.08618835567458115 +SHP099-1 Example 7,Example 8,-11.406924476889998,0.058318227574526565,-6.999332588359879,0.05737165989559677,0.04031999999999947,-4.407591888530119,0.08180784208503668,-4.552883978518599,0.0681524599841816 +SHP836-2,3,1.1172206034815682,0.04449670909979278,1.9202013240149527,0.043353729492096746,1.2502700000000004,-0.8029807205333845,0.06212489824205333,-0.8376656268729317,0.1087554377807606 +SHP836-2,6,-10.968206177341218,0.07235742529871118,-10.22722941253613,0.06731303569183474,-1.3168299999999995,-0.7409767648050889,0.09882632124039015,-0.0684496241518513,0.0943121166831889 diff --git a/summaries/2026_apr_23/merck/shp2/dg_comparison_plot.png b/summaries/2026_apr_23/merck/shp2/dg_comparison_plot.png new file mode 100644 index 0000000..1240201 Binary files /dev/null and b/summaries/2026_apr_23/merck/shp2/dg_comparison_plot.png differ diff --git a/summaries/2026_apr_23/merck/shp2/dg_plot.png b/summaries/2026_apr_23/merck/shp2/dg_plot.png new file mode 100644 index 0000000..778871b Binary files /dev/null and b/summaries/2026_apr_23/merck/shp2/dg_plot.png differ diff --git a/summaries/2026_apr_23/merck/shp2/dg_results.csv b/summaries/2026_apr_23/merck/shp2/dg_results.csv new file mode 100644 index 0000000..8df0fa1 --- /dev/null +++ b/summaries/2026_apr_23/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,-7.819502979834496,0.046845299431659757,-7.15428 +Example 30,CC1([NH3+])CCN(c2nnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-10.329664444166488,0.03844951067120905,-9.1571 +Example 23,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Cl)CC1,-8.381911752724193,0.0517977182513443,-8.74034 +11,CNc1nc(N2CCC(C)([NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-6.446701183405766,0.04070552526798057,-6.35409 +3,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-7.75599685220935,0.07914091880266638,-5.46294 +6,Nc1nc(N2CCC([NH3+])CC2)ncc1-c1cccc(Cl)c1Cl,-6.9867808494882695,0.05770888263784682,-8.03004 +Example 27,C[C@@H]1CN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-7.198979474758742,0.08360965992656845,-8.51853 +4,C[C@@H]1CN(c2ncc(-c3ccc(Cl)c(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-8.139446910288559,0.079985800028165,-5.82207 +SHP836-2,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-6.918331225336418,0.0745953096243635,-6.71321 +7,C[NH+](C)C1CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-6.937217852408633,0.06380762828565789,-7.07647 +Example 14,Nc1nc(N2CC[C@@H](C[NH3+])C2)cnc1-c1cccc(Cl)c1Cl,-12.916018959238905,0.07739208110525768,-9.77823 +Example 9,Nc1nc(N2CCC(C[NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-14.448821866373276,0.0600157440664145,-8.7941 +Example 1,CC1([NH3+])CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-7.926009122937016,0.03984084050260363,-8.98818 +Example 3,CC1([NH3+])CCN(c2ncc(-c3ccc(Cl)s3)c(N)n2)CC1,-8.176858632384702,0.05690019653711617,-8.21587 +Example 4,Cc1ccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)s1,-8.207170479231698,0.0617943490657726,-8.20109 +Example 5,COc1cc(Cl)c(Cl)c(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1,-5.940329070898816,0.05174056869543424,-7.56309 +Example 8,CC1(C[NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-13.79886507427825,0.04545848589938215,-9.71233 +Example 22,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Br)CC1,-7.575295101615453,0.06304204549312704,-9.23883 +Example 24,Cc1nc(-c2cccc(Cl)c2Cl)c(N)nc1N1CCC(C)([NH3+])CC1,-6.596722834102222,0.062214154115139635,-9.07722 +Example 26,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C(N)=O)CC1,-6.683871642356968,0.0620040660891225,-8.95905 +Example 6,CC1([NH3+])CCN(c2ncc(-c3cc(O)cc(Cl)c3Cl)c(N)n2)CC1,-6.583501439831439,0.057964575630404774,-9.06926 +Example 25,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C#N)CC1,-5.369687339609819,0.06228862143727777,-8.86991 +Example 29,CC1([NH3+])CCN(c2cnc(C3=CCCCC3)c(N)n2)CC1,-7.7308685207636865,0.06964300964387565,-7.62278 +Example 28,CC1([NH3+])CCN(c2cnc(-c3cccc4cc[nH]c34)c(N)n2)CC1,-8.95331624033971,0.07436044521049277,-8.45735 +Example 2,Cc1cccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1Cl,-6.53737905565751,0.047243328050700625,-8.27622 +SHP099-1 Example 7,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.245981095759651,0.05077680436607986,-9.75265 diff --git a/summaries/2026_apr_23/miscellaneous_set/cdk8/README.md b/summaries/2026_apr_23/miscellaneous_set/cdk8/README.md new file mode 100644 index 0000000..c490652 --- /dev/null +++ b/summaries/2026_apr_23/miscellaneous_set/cdk8/README.md @@ -0,0 +1,40 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.16 +- RMSE: 1.31 +- R²: 0.02 +- Kendall 𝜏: -0.06 +- Spearman ρ: -0.12 + +## 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: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427) +- GPU: RTX 5090, RTX 50080 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.51 Hours +- Average Time Per Edge: 0.09 Hours +- Total Nanoseconds Simulated: 935.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 422 + - 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_apr_23/miscellaneous_set/cdk8/ddg_results.csv b/summaries/2026_apr_23/miscellaneous_set/cdk8/ddg_results.csv new file mode 100644 index 0000000..9bdb23e --- /dev/null +++ b/summaries/2026_apr_23/miscellaneous_set/cdk8/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) +12,14,-6.077558833296421,0.04095180479541923,-6.418734773386498,0.0380639863898133,-1.1986399999999993,0.3411759400900761,0.05590990409476674,0.34117593951012104,0.05684423206677822 +12,15,5.1849023613846255,0.0464520773077561,5.4523331757360545,0.04664084080155476,0.11278000000000077,-0.2674308143514285,0.06582676899925839,-0.2674308141283994,0.08464059857401607 +12,22,-6.644335134304847,0.05157864814407631,-6.651972387102071,0.05243769329432778,-1.4571400000000008,0.007637252797224201,0.07355316867681783,0.0076372521321630416,0.09396612076409974 +13,19,21.01155585199899,0.04568320054533302,21.031293818088603,0.048108586569390085,0.9724000000000004,-0.01973796608961485,0.06634297938568644,-0.2634365597041324,0.06886945689651941 +13,20,24.47315154380357,0.05101284364143894,25.430821734990317,0.05180411978620089,0.9141000000000012,-0.9576701911867472,0.07270472504046038,-0.6649933548659028,0.07258931074568874 +13,21,31.434833915476364,0.052718804624146284,28.882884167260563,0.04906391439185877,1.3348600000000008,2.5519497482158036,0.07201763712071199,2.5519497481479405,0.0912210482301564 +14,17,13.03494649198366,0.048308354151070446,11.131143760788966,0.047024425659426744,0.6362999999999985,1.9038027311946941,0.06741656835959688,1.9038027309463121,0.07039954373062995 +14,19,8.950576690504887,0.05097708049560846,11.041968614240139,0.04992816620835952,0.8067999999999991,-2.0913919237352525,0.07135463906982725,-1.8094838522403514,0.05995526307789855 +14,20,14.97708675917757,0.049989288798479824,16.930784449499885,0.04635612121660331,0.7484999999999999,-1.9536976903223155,0.06817491451279012,-2.211040647402122,0.06419376536746105 +15,21,,,30.929902668299107,0.06138555540989987,-0.1421600000000005,,,1.614509209250242,0.1053834679892107 +15,22,,,-12.325697569867367,0.05648732177309929,-1.5699200000000015,,,0.27506806626056246,0.10899543601917946 +16,17,,,29.18298913731452,0.05249389307503688,0.24019999999999975,,,, diff --git a/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_comparison_plot.png b/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_comparison_plot.png new file mode 100644 index 0000000..dc2f7ec Binary files /dev/null and b/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_comparison_plot.png differ diff --git a/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_plot.png b/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_plot.png new file mode 100644 index 0000000..ba301cf Binary files /dev/null and b/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_plot.png differ diff --git a/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_results.csv b/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_results.csv new file mode 100644 index 0000000..eca406a --- /dev/null +++ b/summaries/2026_apr_23/miscellaneous_set/cdk8/dg_results.csv @@ -0,0 +1,10 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12,COC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-10.329775052160427,0.04535227505544824,-9.83296 +14,CNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-9.988599112650306,0.03427007246208716,-11.0316 +15,CN(C)C(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-10.597205866288826,0.0714646911017091,-9.72018 +22,CNC(=O)c1cc2c(Oc3ccc(I)cc3)cncc2s1,-10.322137800028264,0.08229704125148331,-11.2901 +13,NC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.534646405186525,0.048195501751078645,-11.1972 +19,CC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.798082964890657,0.04919548459140656,-10.2248 +20,CCC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-12.199639760052428,0.05428076681013209,-10.2831 +21,O=C(c1cc2c(Oc3ccc(Cl)cc3)cncc2s1)C1CC1,-8.982696657038584,0.0774498111758208,-9.86234 +17,O=C(NC1CC1)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-8.084796381703994,0.06149518591665672,-10.3953