diff --git a/summaries/2026_jun_08_abfe/README.md b/summaries/2026_jun_08_abfe/README.md new file mode 100644 index 0000000..8f1f945 --- /dev/null +++ b/summaries/2026_jun_08_abfe/README.md @@ -0,0 +1,13 @@ +# Summary 2026 Jun 08 Abfe +- Number of Datasets: 64 +- Number of Ligands: 1009 +- Total Wallclock Time: 479.57 Hours +- Average Time Per Mol: 0.48 Hours +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) + + +## Description +Initial experimental ABFE workflow benchmarks. + + +![Retrospective dG performance](dg_plot.png) diff --git a/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/README.md b/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/README.md new file mode 100644 index 0000000..c6cf4a8 --- /dev/null +++ b/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/README.md @@ -0,0 +1,33 @@ +# Brd4 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 25.53 +- RMSE: 25.62 +- R²: 0.74 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 2055 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.21 Hours +- Average Time Per Molecule: 0.40 Hours +- Total Nanoseconds Simulated: 534.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_plot.png b/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_plot.png new file mode 100644 index 0000000..10155e1 Binary files /dev/null and b/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_results.csv b/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_results.csv new file mode 100644 index 0000000..3b01728 --- /dev/null +++ b/summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_results.csv @@ -0,0 +1,4 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +61a,47.133297406893405,0.08118288902088129,13.89247731831242,0.07759108444327037,-7.3099318,-40.55075,0.11229887735351338,-12.0 +25e,40.59795440276401,0.08328969751498352,12.771085695082354,0.07998658165716004,-7.295111,-35.121983,0.11547738721210739,-11.3 +11,26.98212087280796,0.06867945587549777,2.3253710642398864,0.0681932167612316,-7.7607136,-32.41746,0.0967842056928648,-8.2 diff --git a/summaries/2026_jun_08_abfe/bayer_macrocycles/ftase/dg_results.csv b/summaries/2026_jun_08_abfe/bayer_macrocycles/ftase/dg_results.csv new file mode 100644 index 0000000..a4515f7 --- /dev/null +++ b/summaries/2026_jun_08_abfe/bayer_macrocycles/ftase/dg_results.csv @@ -0,0 +1,2 @@ +mol,solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol) +"lig 2, deprot",8.533702028703582,0.07501604126636303 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/README.md new file mode 100644 index 0000000..9894fec --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/README.md @@ -0,0 +1,33 @@ +# Cdk2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 18.55 +- RMSE: 18.61 +- R²: 1.00 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 9185 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.33 Hours +- Average Time Per Molecule: 0.78 Hours +- Total Nanoseconds Simulated: 550.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_plot.png new file mode 100644 index 0000000..08b68a6 Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_results.csv new file mode 100644 index 0000000..1d47a37 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_results.csv @@ -0,0 +1,4 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +39charg,90.22546877363595,0.08257582965752981,72.7985889657264,0.08060142733212708,-7.270515,-24.697393,0.1153921909472454,-8.37 +34,40.120661432573996,0.08163805516291812,17.90254854111144,0.076070956990173,-7.3340454,-29.55216,0.11158656974826502,-9.88 +25,37.35436788025175,0.08117936328891588,15.071258833825516,0.07391397208483001,-7.18808,-29.471188,0.10978781486736501,-9.83 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/README.md new file mode 100644 index 0000000..992c27b --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/README.md @@ -0,0 +1,33 @@ +# Dlk + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 23.99 +- RMSE: 24.09 +- R²: 0.17 +- Kendall 𝜏: 0.20 +- Spearman ρ: 0.50 + +## System Details +- Ligands: 5 +- Host Atoms: 4533 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.25 Hours +- Average Time Per Molecule: 0.45 Hours +- Total Nanoseconds Simulated: 896.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_plot.png new file mode 100644 index 0000000..9021bc7 Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_results.csv new file mode 100644 index 0000000..e9124a1 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_results.csv @@ -0,0 +1,6 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +9,35.026483491975654,0.08593518280354508,8.037300899162101,0.07478079102561291,-6.972359,-33.96154,0.1139167342838404,-8.73 +17charg,52.98690536047751,0.08068433816806259,23.511266326311166,0.07788800264088488,-7.150694,-36.62633,0.11214501050427866,-10.44 +4charg,55.71822585363572,0.07995489354658021,30.523484306598295,0.07397497080389523,-6.89343,-32.08817,0.10892695399891675,-9.33 +18,28.242948966055273,0.07678819292738583,4.97515736501246,0.0711212548048987,-6.8783946,-30.146185,0.10466450906623864,-9.98 +8,58.96867681546791,0.0778353080903196,29.81757616258509,0.07657409130421887,-6.9475603,-36.098663,0.10918757550464163,-10.51 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/README.md new file mode 100644 index 0000000..90713b6 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/README.md @@ -0,0 +1,33 @@ +# Egfr + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 41.00 +- RMSE: 41.42 +- R²: 0.27 +- Kendall 𝜏: -0.20 +- Spearman ρ: -0.50 + +## System Details +- Ligands: 5 +- Host Atoms: 4370 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.95 Hours +- Average Time Per Molecule: 0.59 Hours +- Total Nanoseconds Simulated: 1034.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_plot.png new file mode 100644 index 0000000..7d7d5bb Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_results.csv new file mode 100644 index 0000000..ffbd5f0 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_results.csv @@ -0,0 +1,6 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +21,57.400029051999944,0.09132418607457905,12.931671895848307,0.08291253968333541,-7.8553395,-52.3237,0.12334746125853181,-9.88 +27chargR,74.80616070688536,0.09333836759198591,26.55747864714727,0.08460785441844565,-7.6062083,-55.854893,0.12597833104954828,-9.94 +28charg,63.60238286762049,0.09101379712983966,28.105795184510207,0.08623956590877757,-6.9341555,-42.430744,0.1253825107266799,-10.7 +29charg,73.96797510438594,0.0908750798899253,23.116007623435074,0.08561037278727247,-7.4772835,-58.329247,0.12484957378291714,-10.46 +30charg,72.92636113291925,0.08855975079784091,32.22275115825482,0.08383245754314463,-7.5865097,-48.29012,0.12194552225932215,-11.25 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/README.md new file mode 100644 index 0000000..86252a8 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/README.md @@ -0,0 +1,33 @@ +# Ephx2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 26.29 +- RMSE: 26.98 +- R²: 0.53 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.40 + +## System Details +- Ligands: 4 +- Host Atoms: 5004 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.78 Hours +- Average Time Per Molecule: 0.45 Hours +- Total Nanoseconds Simulated: 722.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_plot.png new file mode 100644 index 0000000..76e0041 Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_results.csv new file mode 100644 index 0000000..37cde7f --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_results.csv @@ -0,0 +1,5 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +47charg,98.70007055354246,0.08683092418291108,67.60929140004637,0.08021258031002756,-7.792158,-38.88293,0.11821026788926195,-11.25 +19charg,83.22333632601699,0.08082503565845169,66.79436640823026,0.07491627141433276,-7.8680663,-24.297039,0.11020496409788424,-8.24 +20,44.78692274491288,0.0756835330064449,11.781804223041359,0.06958230898597266,-7.4026423,-40.40776,0.10280902145316337,-9.14 +33,41.90383152725358,0.07978697310188886,8.15782367321106,0.07273924290517396,-7.208311,-40.95432,0.1079673957043488,-10.74 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/README.md new file mode 100644 index 0000000..aa92548 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/README.md @@ -0,0 +1,33 @@ +# Itk + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 27.26 +- RMSE: 27.32 +- R²: 0.12 +- Kendall 𝜏: -0.67 +- Spearman ρ: -0.80 + +## System Details +- Ligands: 4 +- Host Atoms: 4776 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.32 Hours +- Average Time Per Molecule: 0.58 Hours +- Total Nanoseconds Simulated: 774.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_plot.png new file mode 100644 index 0000000..7da964f Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_results.csv new file mode 100644 index 0000000..497180d --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_results.csv @@ -0,0 +1,5 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,47.190611963937435,0.0824590236592623,14.159034333927753,0.08007559183959109,-6.93884,-39.97042,0.11494168517687378,-11.27 +1charg,50.912408499563945,0.08295323355944069,15.894317650916204,0.07852629743075348,-6.9213767,-41.93947,0.11422617189659416,-12.57 +18,45.46220681023861,0.08469769907591107,13.241195453954333,0.07960645511925729,-6.9375086,-39.158516,0.11623634511377202,-12.77 +19,45.294751493131585,0.08470954376613792,14.58804697040108,0.07902528875453034,-6.9255776,-37.632282,0.11584775814751071,-13.07 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/README.md new file mode 100644 index 0000000..2fe0a1b --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/README.md @@ -0,0 +1,33 @@ +# Jak1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 22.92 +- RMSE: 23.08 +- R²: 0.06 +- Kendall 𝜏: -0.47 +- Spearman ρ: -0.66 + +## System Details +- Ligands: 6 +- Host Atoms: 5100 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.84 Hours +- Average Time Per Molecule: 0.47 Hours +- Total Nanoseconds Simulated: 1027.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_plot.png new file mode 100644 index 0000000..9c24d9e Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_results.csv new file mode 100644 index 0000000..c01cdb0 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_results.csv @@ -0,0 +1,7 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,37.010694505291646,0.07196406120222455,10.389070631019946,0.06628909785740457,-7.2666197,-33.888245,0.0978420696810226,-10.87 +18charg,65.00809318123508,0.08058107553062685,33.98920029375755,0.07440793936518929,-7.386954,-38.405846,0.10968067821747947,-11.3 +jmc_25,31.77132570974772,0.079452121417108,8.382902989300252,0.07238645892984602,-7.3067875,-30.69521,0.10748227311552895,-11.41 +jmc_34,35.79026741372582,0.08320798926447061,9.492117602481525,0.0728836575156549,-7.19204,-33.49019,0.1106146328940956,-13.07 +16charg,67.21216301363843,0.07473884974251271,38.748290906807696,0.0726998237272144,-7.249262,-35.713135,0.10426485520443568,-10.54 +jmc_22,39.11280926200088,0.07901860535106717,12.48755331236636,0.07068068225270892,-7.2712975,-33.896553,0.10601744590083323,-11.35 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/README.md new file mode 100644 index 0000000..14c9a0c --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/README.md @@ -0,0 +1,33 @@ +# Jnk1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.17 +- RMSE: 21.34 +- R²: 0.01 +- Kendall 𝜏: -0.33 +- Spearman ρ: -0.50 + +## System Details +- Ligands: 3 +- Host Atoms: 5993 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.36 Hours +- Average Time Per Molecule: 0.45 Hours +- Total Nanoseconds Simulated: 496.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_plot.png new file mode 100644 index 0000000..053d059 Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_results.csv new file mode 100644 index 0000000..da80777 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_results.csv @@ -0,0 +1,4 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +6a,35.05677176705646,0.06818299316838441,12.323812260514739,0.06624380490768736,-7.4312205,-30.164179,0.09506399026996341,-8.41 +19b_charg,92.76071946815068,0.07721219722133342,75.22082016432068,0.07331111024121917,-7.3782635,-24.918163,0.10647179102723069,-7.3 +19a_charg,49.248852545944395,0.07300066516742226,25.56239904327995,0.07147454412842849,-7.318644,-31.005096,0.10216509958519479,-6.86 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/README.md new file mode 100644 index 0000000..adcad9b --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/README.md @@ -0,0 +1,33 @@ +# Ptp1B + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 29.10 +- RMSE: 29.55 +- R²: 0.52 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.50 + +## System Details +- Ligands: 3 +- Host Atoms: 5163 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.79 Hours +- Average Time Per Molecule: 0.60 Hours +- Total Nanoseconds Simulated: 656.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_plot.png new file mode 100644 index 0000000..b8fa231 Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_results.csv new file mode 100644 index 0000000..591f68f --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_results.csv @@ -0,0 +1,4 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +26charg,102.1946467041906,0.08576447016244779,72.71683462498555,0.07995209903654799,-7.148156,-36.625973,0.11725136452338358,-7.44 +27,171.313708477713,0.09583506472463406,146.81549570771816,0.08751470413881678,-7.4514866,-31.949686,0.12978128937285002,-9.23 +32,190.0950039528491,0.11207762077789028,149.96070686682273,0.08990471319833117,-6.7815003,-46.915787,0.1436810722903569,-11.53 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/README.md new file mode 100644 index 0000000..959208c --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/README.md @@ -0,0 +1,33 @@ +# Thrombin + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 30.41 +- RMSE: 31.06 +- R²: 0.50 +- Kendall 𝜏: -0.20 +- Spearman ρ: -0.09 + +## System Details +- Ligands: 6 +- Host Atoms: 5904 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.00 Hours +- Average Time Per Molecule: 0.50 Hours +- Total Nanoseconds Simulated: 1173.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/dg_plot.png new file mode 100644 index 0000000..b83ef1d Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/dg_results.csv new file mode 100644 index 0000000..94d5a0e --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/thrombin/dg_results.csv @@ -0,0 +1,7 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,73.94265419212486,0.08409739250488471,42.802403485958365,0.07901741375941188,-7.3018966,-38.442154,0.115395507292731,-5.84 +1,39.76443585786778,0.08329568392048418,17.7475171379136,0.07606328749282314,-7.3824487,-29.399368,0.11279979904236122,-6.8 +3,75.12988466144212,0.08493783757286634,42.970414550026604,0.08050492699158204,-7.480527,-39.64,0.11702768698677497,-5.66 +jmb2009-4,93.19912636921222,0.0909532238672236,47.90230568620857,0.0819319501913059,-7.351616,-52.648438,0.1224145963273658,-11.53 +10,44.51248603469551,0.08121960405967268,19.929695379014962,0.07778043527073057,-7.260045,-31.84283,0.11245630348946345,-7.669999999999999 +2,47.481578559868744,0.08453516088935562,20.673862019236992,0.07619596882417787,-7.349091,-34.156807,0.113806937801016,-6.14 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/README.md b/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/README.md new file mode 100644 index 0000000..3db621d --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/README.md @@ -0,0 +1,33 @@ +# Tyk2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 18.98 +- RMSE: 19.42 +- R²: 0.06 +- Kendall 𝜏: -0.40 +- Spearman ρ: -0.50 + +## System Details +- Ligands: 5 +- Host Atoms: 4670 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.25 Hours +- Average Time Per Molecule: 0.45 Hours +- Total Nanoseconds Simulated: 880.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/dg_plot.png b/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/dg_plot.png new file mode 100644 index 0000000..90ed6e7 Binary files /dev/null and b/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/dg_results.csv b/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/dg_results.csv new file mode 100644 index 0000000..e2f5793 --- /dev/null +++ b/summaries/2026_jun_08_abfe/charge_annihilation_set/tyk2/dg_results.csv @@ -0,0 +1,6 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +ejm_47,29.116815870740997,0.07535230944788714,6.8372655364768695,0.07015824795421753,-6.9731903,-29.252743,0.10295703130498475,-9.79 +jmc_32charg,84.03717835010869,0.08312121282977375,67.77936201164529,0.07771531462629194,-6.996643,-23.25446,0.11379282116968578,-11.66 +jmc_31,43.57925821765423,0.07372768385904688,16.389670008695226,0.07562374706214448,-6.9434643,-34.13305,0.10561591966620736,-10.92 +ejm_52charg,58.66161602749671,0.07840468398140714,35.747585812034,0.07470167743970238,-6.969779,-29.883806,0.10829420613555307,-7.49 +ejm_46,29.990095281152584,0.07578667380553716,7.266407890768715,0.07100889945872009,-6.925885,-29.649574,0.10385510930544299,-11.42 diff --git a/summaries/2026_jun_08_abfe/dg_plot.png b/summaries/2026_jun_08_abfe/dg_plot.png new file mode 100644 index 0000000..6d483cf Binary files /dev/null and b/summaries/2026_jun_08_abfe/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/README.md b/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/README.md new file mode 100644 index 0000000..2c7ad9e --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/README.md @@ -0,0 +1,33 @@ +# Hsp90 2Rings + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 20.78 +- RMSE: 21.01 +- R²: 0.00 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.09 + +## System Details +- Ligands: 6 +- Host Atoms: 3795 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.34 Hours +- Average Time Per Molecule: 0.39 Hours +- Total Nanoseconds Simulated: 1035.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/dg_plot.png new file mode 100644 index 0000000..f3ed4ba Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/dg_results.csv new file mode 100644 index 0000000..a86c230 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/hsp90_2rings/dg_results.csv @@ -0,0 +1,7 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +18,36.801121323776336,0.07529822873351164,9.614962613406224,0.0734889728685292,-7.582553,-34.76871,0.10521621730358709,-8.96 +17,37.744098222621034,0.07851331977917415,13.53661381666555,0.0758833295323864,-7.484075,-31.69156,0.10919075548629383,-9.92 +19,34.88553443360182,0.07720557066499222,12.774931464593902,0.07407921468975116,-7.623622,-29.734222,0.10699733730685708,-10.26 +15,29.030883319424074,0.07651259271663709,10.733997256237311,0.07479616272902599,-7.594443,-25.89133,0.10699833084309737,-9.88 +14,35.55834984531621,0.07738738009686251,11.826438921168517,0.07344337931957606,-7.7178245,-31.449736,0.10668990844562293,-8.72 +16,33.52197347626841,0.07797834187161773,14.203517024310486,0.07238676469547321,-7.675343,-26.993797,0.10639767621581168,-8.12 diff --git a/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/README.md b/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/README.md new file mode 100644 index 0000000..544b964 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/README.md @@ -0,0 +1,33 @@ +# Hsp90 Single Ring + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 18.65 +- RMSE: 18.80 +- R²: 0.02 +- Kendall 𝜏: 0.00 +- Spearman ρ: 0.05 + +## System Details +- Ligands: 7 +- Host Atoms: 3795 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.40 Hours +- Average Time Per Molecule: 0.34 Hours +- Total Nanoseconds Simulated: 1082.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/dg_plot.png new file mode 100644 index 0000000..944a026 Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/dg_results.csv new file mode 100644 index 0000000..1026395 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/hsp90_single_ring/dg_results.csv @@ -0,0 +1,8 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,29.459571135943175,0.07041786063262549,8.258200213288909,0.0683755283941327,-7.607222,-28.808594,0.09815237123601607,-8.31 +3,24.72041492523567,0.07628947774784978,9.177585467713259,0.0684957884779784,-7.6822195,-23.225048,0.10252686211066651,-8.31 +9,29.991307070580906,0.06907552003228529,9.1446300891992,0.06842085503581477,-7.683227,-28.529903,0.09722572124475408,-7.36 +8,29.476033784406653,0.08426622769869645,13.469614699464564,0.0691208510389979,-7.675138,-23.681557,0.10898848186356158,-8.03 +11,33.96532444048908,0.07249086103308891,12.54583259949356,0.06734659923257531,-7.706841,-29.126333,0.09894690172770303,-8.12 +12,31.820717452554717,0.07190956329880206,11.449380231185254,0.06860109304549396,-7.598116,-27.969452,0.09938357641411853,-8.59 +2,27.151125156918507,0.0693667474066962,9.880184056732986,0.06613576579504235,-7.5713906,-24.84233,0.0958419801709099,-6.93 diff --git a/summaries/2026_jun_08_abfe/fragments/jak2_set1/README.md b/summaries/2026_jun_08_abfe/fragments/jak2_set1/README.md new file mode 100644 index 0000000..1c72105 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/jak2_set1/README.md @@ -0,0 +1,33 @@ +# Jak2 Set1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 19.27 +- RMSE: 19.35 +- R²: 0.76 +- Kendall 𝜏: 0.64 +- Spearman ρ: 0.81 + +## System Details +- Ligands: 10 +- Host Atoms: 5622 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.50 Hours +- Average Time Per Molecule: 0.35 Hours +- Total Nanoseconds Simulated: 1398.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/jak2_set1/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/jak2_set1/dg_plot.png new file mode 100644 index 0000000..fdbde8e Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/jak2_set1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/jak2_set1/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/jak2_set1/dg_results.csv new file mode 100644 index 0000000..8491459 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/jak2_set1/dg_results.csv @@ -0,0 +1,11 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2_3E63,31.005155482802206,0.06516334999250448,9.89049724005105,0.0643416264807681,-7.811322,-28.925982,0.09157569044476985,-7.90701 +9,28.481720013851017,0.06880909320710646,9.279880069396699,0.06429047643306643,-7.53172,-26.73356,0.09416982886240655,-8.36388 +8,29.808329520964076,0.06676293141791807,8.902294609066823,0.0661829786213556,-7.967141,-28.873175,0.0940078489845845,-8.77456 +5,32.336654279805416,0.0664664745869928,13.041852117907355,0.06342107690240406,-7.9022784,-27.197077,0.09186960998874442,-7.7898000000000005 +10,31.729212368457592,0.06524161673027865,11.918566246409156,0.06576264021972868,-7.376193,-27.186836,0.09263473107992515,-7.14398 +4a,36.49123928860092,0.06481635475734907,16.108127420947387,0.06285898980276586,-7.9750686,-28.358183,0.09029071072405373,-6.86423 +6,26.38717443681882,0.06819302301825786,10.337029899762134,0.06428340150328218,-7.4593334,-23.509476,0.09371576226655165,-6.19864 +3,25.196317333398728,0.06883000827177205,10.023194224824323,0.06286954039752522,-7.3665557,-22.539679,0.09322096946764855,-5.23562 +1_3E62,24.15654625783873,0.06202869970226631,8.995302784131768,0.0588068844223396,-6.950141,-22.111382,0.08547402671113806,-5.98669 +7,32.618553443827295,0.07180446217926564,10.125072278462792,0.06470838548964768,-7.8643494,-30.35783,0.09665948448823031,-8.86058 diff --git a/summaries/2026_jun_08_abfe/fragments/jak2_set2/README.md b/summaries/2026_jun_08_abfe/fragments/jak2_set2/README.md new file mode 100644 index 0000000..c5dab6c --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/jak2_set2/README.md @@ -0,0 +1,33 @@ +# Jak2 Set2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 18.95 +- RMSE: 19.15 +- R²: 0.40 +- Kendall 𝜏: 0.57 +- Spearman ρ: 0.74 + +## System Details +- Ligands: 8 +- Host Atoms: 5857 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.69 Hours +- Average Time Per Molecule: 0.46 Hours +- Total Nanoseconds Simulated: 1412.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/jak2_set2/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/jak2_set2/dg_plot.png new file mode 100644 index 0000000..35a7054 Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/jak2_set2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/jak2_set2/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/jak2_set2/dg_results.csv new file mode 100644 index 0000000..fde7df7 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/jak2_set2/dg_results.csv @@ -0,0 +1,9 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +13_3E64,39.976249445041816,0.0800770735372223,20.6305086081694,0.0729503051666894,-7.083266,-26.429005,0.10832398040230437,-9.69694 +21,44.06327842635486,0.08107193451856519,19.670862060154263,0.07548273089196308,-7.249687,-31.642103,0.1107713917466556,-8.34034 +20,37.327887163889336,0.08260660301096118,18.68701608062364,0.07497950894442588,-7.004755,-25.645626,0.11156064549184798,-8.06767 +18,37.1097307650926,0.07991208915371348,18.220530729847802,0.0710534854728857,-7.6007123,-26.489912,0.10693240757953891,-8.32514 +14,34.78721684190489,0.07635860543160462,13.754861587718597,0.07133909697042362,-7.06758,-28.099936,0.10449834151801159,-7.7898000000000005 +12,35.01144966244897,0.08051358525754371,19.86729225737652,0.0735765811743888,-7.100806,-22.244965,0.10906855966929785,-7.43483 +15,32.50755855951753,0.07912547892268366,14.469723615192105,0.0738401150767155,-7.0836797,-25.121517,0.10822755660776347,-7.37912 +22-flip,44.887309414868454,0.08023362004563912,18.908373277047502,0.07476770787313423,-7.063835,-33.04277,0.10967061560067182,-10.1076 diff --git a/summaries/2026_jun_08_abfe/fragments/liga/README.md b/summaries/2026_jun_08_abfe/fragments/liga/README.md new file mode 100644 index 0000000..745de06 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/liga/README.md @@ -0,0 +1,33 @@ +# Liga + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.15 +- RMSE: 21.42 +- R²: 0.84 +- Kendall 𝜏: 0.64 +- Spearman ρ: 0.79 + +## System Details +- Ligands: 11 +- Host Atoms: 5824 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.48 Hours +- Average Time Per Molecule: 0.41 Hours +- Total Nanoseconds Simulated: 1552.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/liga/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/liga/dg_plot.png new file mode 100644 index 0000000..fe48734 Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/liga/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/liga/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/liga/dg_results.csv new file mode 100644 index 0000000..5528375 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/liga/dg_results.csv @@ -0,0 +1,12 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12,44.51387315834883,0.0746061315324264,13.80992955171263,0.07085147046176177,-7.1881523,-37.892094,0.10288831677516942,-9.05 +9,27.607448548504877,0.06602731110752519,8.391821611006387,0.06291941491796804,-7.1835566,-26.399183,0.09120558418051682,-6.38 +5,26.54445094069878,0.06228409730182867,11.067675716322366,0.05813974341914955,-7.2193527,-22.696129,0.08520292566307923,-4.8 +6,28.203882711498327,0.06554248596378465,10.590122858240887,0.062024234490374884,-7.1671977,-24.780956,0.09023759266752364,-5.3 +11,33.86630162603168,0.0683757105377578,7.121790014853662,0.0656406525757549,-7.143222,-33.887737,0.09478361178027667,-9.08 +10,29.937976068027485,0.06549685779286495,8.903447873912617,0.05992207148121789,-7.1698523,-28.20438,0.08877214107668553,-6.54 +8,28.416419367929976,0.06457053780825149,8.638594297768325,0.06262412889863553,-7.185345,-26.963173,0.0899507413708178,-5.83 +3,29.48010528572967,0.064278530962608,12.320852420599925,0.05935360587225736,-7.271537,-24.430788,0.08749045703818342,-6.03 +7,27.18790626321361,0.08668957063199542,10.34036193401888,0.06050676882293758,-7.287821,-24.135365,0.10571731518418416,-5.25 +13,42.58081033153589,0.07645077115289181,14.670464061941288,0.06936842375879092,-7.16799,-35.078335,0.10323128704346866,-10.67 +4,26.98340408444784,0.06260632153921464,10.588890429589929,0.060502256511618446,-7.2095003,-23.604013,0.08706362351561764,-6.5 diff --git a/summaries/2026_jun_08_abfe/fragments/mcl1/README.md b/summaries/2026_jun_08_abfe/fragments/mcl1/README.md new file mode 100644 index 0000000..3d5a95f --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/mcl1/README.md @@ -0,0 +1,33 @@ +# Mcl1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 18.23 +- RMSE: 18.41 +- R²: 0.00 +- Kendall 𝜏: 0.03 +- Spearman ρ: 0.07 + +## System Details +- Ligands: 12 +- Host Atoms: 2428 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.05 Hours +- Average Time Per Molecule: 0.34 Hours +- Total Nanoseconds Simulated: 1916.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/mcl1/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/mcl1/dg_plot.png new file mode 100644 index 0000000..b3b5c3b Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/mcl1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/mcl1/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/mcl1/dg_results.csv new file mode 100644 index 0000000..cfa61c9 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/mcl1/dg_results.csv @@ -0,0 +1,13 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2,73.84702998280152,0.07209224256009315,57.05993438875728,0.06682180943458693,-7.3215227,-24.108616,0.0982977398186528,-5.33 +3,74.99303228353415,0.07014616190201287,54.713513078386285,0.06885114039860758,-7.2558284,-27.535349,0.0982902007515102,-6.39 +4,70.73526498357336,0.07665816928517037,54.79797948125444,0.06724979480283384,-6.796447,-22.733736,0.10197553539539321,-5.81 +5,69.30813719631115,0.07214916688320673,56.11137925223776,0.0665806679578073,-6.8395424,-20.036303,0.09817579960279725,-6.04 +7,70.36443122192594,0.06942653638521668,54.555070546303085,0.06773561782691397,-6.912141,-22.721508,0.09699565906184442,-5.88 +8,70.71763366194229,0.08293685060052261,54.48727698175074,0.06629875090760542,-6.836124,-23.066483,0.10617930852780177,-6.37 +9,76.33912314181688,0.07238490147184601,57.686276626920694,0.07006967015911901,-7.455737,-26.108583,0.10074389627811994,-5.48 +10,70.70161710664613,0.08200887255450733,57.18237554306246,0.06833282386985316,-6.824673,-20.343916,0.10674656901132606,-5.04 +11,67.55576817811867,0.06848760016312604,50.37400572635948,0.06680068932448978,-7.023426,-24.205185,0.09567070330216677,-5.55 +14,73.88899204244282,0.07171945494837938,56.69651852616265,0.06839981594456682,-7.758332,-24.950811,0.09910708874416217,-5.61 +15,78.45553250352444,0.0715022797439298,56.92466022994275,0.07244240349674348,-7.4428287,-28.973701,0.10178643246014758,-5.31 +13 flipped,75.85296787145052,0.07189430303166537,61.123849583560336,0.06856638243401722,-7.2802024,-22.009315,0.09934857627815727,-5.21 diff --git a/summaries/2026_jun_08_abfe/fragments/mup1/README.md b/summaries/2026_jun_08_abfe/fragments/mup1/README.md new file mode 100644 index 0000000..d05f1ff --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/mup1/README.md @@ -0,0 +1,33 @@ +# Mup1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.26 +- RMSE: 21.30 +- R²: 0.19 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.80 + +## System Details +- Ligands: 6 +- Host Atoms: 2486 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.07 Hours +- Average Time Per Molecule: 0.18 Hours +- Total Nanoseconds Simulated: 532.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/mup1/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/mup1/dg_plot.png new file mode 100644 index 0000000..99fdf3a Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/mup1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/mup1/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/mup1/dg_results.csv new file mode 100644 index 0000000..8f10ce9 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/mup1/dg_results.csv @@ -0,0 +1,7 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +IBT,20.422981858114788,0.05705376673995692,-2.7743723818421877,0.05877798388287415,-7.677943,-30.875296,0.0819144901012808,-9.09 +MT,,,-0.12202806272054849,0.05349532823468538,,,,-5.64 +PT,17.486158039548126,0.05382247412434938,-1.7413234255594705,0.05600543226563603,-7.874475,-27.101955,0.07767539613112381,-8.2 +SBT_S,19.998994548080677,0.05926093836789466,-2.772581062319772,0.05788188127911995,-7.8413844,-30.61296,0.08283822183420855,-8.42 +IPT,20.30662855685592,0.05211467186073177,-1.8178109664296764,0.056262520174780006,-7.8842087,-30.00865,0.07669035271511844,-7.85 +ET,,,-1.066939425301525,0.05450670896500637,,,,-6.96 diff --git a/summaries/2026_jun_08_abfe/fragments/p38/README.md b/summaries/2026_jun_08_abfe/fragments/p38/README.md new file mode 100644 index 0000000..340c2b6 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/p38/README.md @@ -0,0 +1,33 @@ +# P38 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 22.77 +- RMSE: 22.87 +- R²: 0.79 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.77 + +## System Details +- Ligands: 6 +- Host Atoms: 7065 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.70 Hours +- Average Time Per Molecule: 0.45 Hours +- Total Nanoseconds Simulated: 884.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/p38/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/p38/dg_plot.png new file mode 100644 index 0000000..2477536 Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/p38/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/p38/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/p38/dg_results.csv new file mode 100644 index 0000000..2dc4b2d --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/p38/dg_results.csv @@ -0,0 +1,7 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +4,28.01185435341028,0.06738676691636968,3.757109520744018,0.06432903299197933,-7.2921314,-31.546879,0.09316222861827801,-5.4 +1_1W7H,22.33980283237735,0.06835784400184179,4.584602645618285,0.06394702736821713,-6.791109,-24.54631,0.09360564697608605,-3.94 +6,25.335121586468492,0.07366691967005332,4.92879108734914,0.06934808454383631,-7.045136,-27.451468,0.10117298000737725,-5.04 +5_1WBW,27.42667806650814,0.07344243085102684,5.459196526247501,0.06641757469405869,-7.202443,-29.169926,0.09902062854551431,-5.94 +7,25.712726592278006,0.07981609343440202,1.8869846938417785,0.07012972117468208,-6.872709,-30.698452,0.10624870146579603,-6.3 +3,17.4005114293993,0.06701146878927836,0.7877372864470414,0.061505497563421836,-7.3004193,-23.913195,0.0909585794734093,-4.09 diff --git a/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/README.md b/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/README.md new file mode 100644 index 0000000..c597bae --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/README.md @@ -0,0 +1,33 @@ +# T4 Lysozyme + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 16.73 +- RMSE: 16.82 +- R²: 0.48 +- Kendall 𝜏: 0.45 +- Spearman ρ: 0.64 + +## System Details +- Ligands: 12 +- Host Atoms: 2609 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.76 Hours +- Average Time Per Molecule: 0.23 Hours +- Total Nanoseconds Simulated: 1276.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/dg_plot.png b/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/dg_plot.png new file mode 100644 index 0000000..1cb5dbd Binary files /dev/null and b/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/dg_results.csv b/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/dg_results.csv new file mode 100644 index 0000000..8532d88 --- /dev/null +++ b/summaries/2026_jun_08_abfe/fragments/t4_lysozyme/dg_results.csv @@ -0,0 +1,13 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +meta methyl ethyl benzene,13.154417414406655,0.05529641076135043,-4.056124917100958,0.05637784664670289,-6.9253707,-24.135912,0.078969327182186,-5.08 +methyl benzene,11.75912962960728,0.05082117404922853,-2.618642789117512,0.053122721705491496,-6.8659706,-21.243742,0.07351744890256377,-5.48 +ethyl benzene,12.6227862269049,0.048242493282664646,-3.4929996177922153,0.056149733983181474,-7.4920993,-23.607883,0.07402790544456858,-5.72 +ortho methyl ethyl benzene,9.330778339980256,0.05421290316400442,-4.060362331641343,0.055691629303696956,-7.721061,-21.112202,0.07772127407582893,-4.53 +m-xylene,8.523997969208272,0.05430108996541434,-3.3821913070543617,0.05457566004672829,-6.592643,-18.49883,0.07698773305513079,-4.72 +p-xylene,11.745599529515136,0.059620779842587845,-3.327751943237583,0.054278180342558394,-6.714979,-21.78833,0.08062727981482212,-4.63 +o-xylene,7.90258730017476,0.061461320111480304,-3.209943314309821,0.054148995749281385,-6.7844744,-17.897005,0.08191219451645491,-4.57 +butyl benzene,12.379475394237254,0.05293899458414269,-5.126240790202054,0.06013178741429509,-7.718276,-25.223991,0.08011472402260315,-6.66 +propyl benzene,11.081785427831154,0.056240282533246526,-4.242362254614327,0.05611829791851362,-7.8582745,-23.182423,0.07944956098488173,-6.51 +para methyl ethyl benzene,12.545313253691468,0.05166389749825061,-4.1084487668635825,0.056140681806806814,-7.7171474,-24.37091,0.07629504871512224,-5.38 +benzene,10.99102670625848,0.04873180539701735,-2.0529187230274015,0.05024774613388668,-7.91124,-20.955185,0.06999732029719632,-5.16 +isobutyl benzene,11.66225940083748,0.05975451674150287,-4.956117794775955,0.05664368317112104,-6.946136,-23.564514,0.08233534547325887,-6.44 diff --git a/summaries/2026_jun_08_abfe/gpcrs/a2a/README.md b/summaries/2026_jun_08_abfe/gpcrs/a2a/README.md new file mode 100644 index 0000000..2426aeb --- /dev/null +++ b/summaries/2026_jun_08_abfe/gpcrs/a2a/README.md @@ -0,0 +1,33 @@ +# A2A + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 29.27 +- RMSE: 29.49 +- R²: 0.14 +- Kendall 𝜏: 0.25 +- Spearman ρ: 0.38 + +## System Details +- Ligands: 25 +- Host Atoms: 4651 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 11.30 Hours +- Average Time Per Molecule: 0.45 Hours +- Total Nanoseconds Simulated: 3721.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/gpcrs/a2a/dg_plot.png b/summaries/2026_jun_08_abfe/gpcrs/a2a/dg_plot.png new file mode 100644 index 0000000..5593e32 Binary files /dev/null and b/summaries/2026_jun_08_abfe/gpcrs/a2a/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/gpcrs/a2a/dg_results.csv b/summaries/2026_jun_08_abfe/gpcrs/a2a/dg_results.csv new file mode 100644 index 0000000..860c448 --- /dev/null +++ b/summaries/2026_jun_08_abfe/gpcrs/a2a/dg_results.csv @@ -0,0 +1,26 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +4g,40.558379629238644,0.07052710569835141,8.279478489748888,0.06831926927787794,-7.4838433,-39.762745,0.09819162486103196,-11.064 +4h,42.645363213874255,0.07166101393396049,7.1673502629487915,0.0704583338310411,-6.794054,-42.272068,0.10049715281683214,-10.6548 +4jS,47.173586861181526,0.07053197122556286,6.787702603444665,0.06982808125576472,-7.6176057,-48.003487,0.09925079292794242,-10.8867 +4jR,36.82064539178185,0.07341878127901325,6.960688346787789,0.06850558068654528,-7.5715055,-37.431465,0.10041579571808587,-10.8867 +4kU,45.12866042157131,0.07380485436726437,6.2337559457609,0.0692169979898807,-6.911554,-45.806458,0.10118374048682058,-11.5415 +4lD,41.113458588960306,0.0676211666874376,5.921625695006993,0.06989092280349503,-7.325341,-42.517174,0.09724897569894668,-11.3778 +4lU,40.822492807117335,0.0666456102365675,5.768001618725386,0.07003220204903032,-7.4418793,-42.496372,0.09667547097191033,-11.3778 +4i,36.987044580888394,0.07204692173777562,6.071508230692481,0.06938099328587187,-7.483153,-38.398693,0.10002240329657831,-10.3137 +4kD,42.317559200406734,0.06872061759958707,6.054255557191277,0.06933154313059739,-7.53923,-43.802536,0.09761857485201555,-11.5415 +4a,38.51626487108211,0.06629229527890204,6.858170765375833,0.06568675928687281,-6.8891196,-38.54722,0.09332426672070192,-9.4133 +4b D,39.25135656688529,0.06695466149405646,5.721488314769845,0.06635371661105446,-6.8271413,-40.35701,0.09426421592462228,-9.959 +4b U,34.2012467363255,0.07332734848781979,5.544433205758445,0.06767803188568124,-7.792438,-36.449253,0.09978585088164281,-9.959 +4c,32.562439009547155,0.07220123912937439,4.510456978644759,0.06735339399008,-7.586991,-35.638973,0.09873954939030281,-11.4597 +4d,35.80393969104961,0.06986998228003698,4.815555545740999,0.06996261498626392,-6.814613,-37.802998,0.09887659945370736,-10.5047 +4o,42.727763220939906,0.06474426868869555,12.16282674340712,0.06738646711012233,-7.5435734,-38.108513,0.09344921764047896,-11.3567 +4f,47.12738565604513,0.06803813437530049,9.139204356763665,0.06889910926191102,-7.5626674,-45.550846,0.09683116743257926,-11.446 +4e U,41.914108934315934,0.071155081663106,9.038510558203429,0.06886932391898891,-7.4965034,-40.372105,0.09902539787116184,-12.0736 +4e D,37.44608769033456,0.06444576859341848,9.46967487908676,0.06985418222288886,-7.576337,-35.552753,0.09504137974390421,-12.0736 +4m U,40.029244790567375,0.06570039396360992,9.225507997080875,0.06674847663031591,-7.825121,-38.628857,0.09365842674015713,-10.5504 +4m D,38.73188154399299,0.06657499240719206,8.914427397653935,0.06666111691428835,-7.6200714,-37.437527,0.09421217608291457,-10.5504 +4q,42.55878438233429,0.06213189318992462,9.81550804838558,0.06662409853120803,-7.565892,-40.30917,0.09109963038596983,-8.8867 +4n,41.07923329098311,0.07173679658269223,8.164914161362134,0.06783832381278464,-7.543632,-40.457954,0.09873300441936722,-11.5504 +4r U,44.717217949210976,0.06698124386214448,6.266389540621866,0.067577058120697,-7.466972,-45.917797,0.09514802054466572,-11.462 +4r D,39.67416236190439,0.0730370842662883,5.6752345455291096,0.06878719577772874,-7.474303,-41.47323,0.10032992565074729,-11.462 +4a flipped,30.46682088464996,0.06801061739518677,6.762117130090109,0.06694555496643145,-6.743158,-30.447863,0.09543139634437911,-9.4133 diff --git a/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/README.md b/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/README.md new file mode 100644 index 0000000..eb70f88 --- /dev/null +++ b/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/README.md @@ -0,0 +1,33 @@ +# P2Y1 Meta Sub + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 13.45 +- RMSE: 13.56 +- R²: 0.07 +- Kendall 𝜏: 0.13 +- Spearman ρ: 0.22 + +## System Details +- Ligands: 20 +- Host Atoms: 4820 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 9.65 Hours +- Average Time Per Molecule: 0.48 Hours +- Total Nanoseconds Simulated: 3626.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/dg_plot.png b/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/dg_plot.png new file mode 100644 index 0000000..92cd9d9 Binary files /dev/null and b/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/dg_results.csv b/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/dg_results.csv new file mode 100644 index 0000000..a495a70 --- /dev/null +++ b/summaries/2026_jun_08_abfe/gpcrs/p2y1_meta_sub/dg_results.csv @@ -0,0 +1,21 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11a,21.085038958807456,0.07819949152435292,6.587224271078249,0.07109474133020013,-7.3640733,-21.861887,0.1056864358348573,-7.774799999999999 +6g,20.560826500726694,0.07935119620848693,6.545878298601441,0.07259753626523016,-7.474293,-21.489243,0.10755005630635067,-9.76958 +6a,20.078465209188142,0.08245981443077507,6.354976269813746,0.07250592182476366,-7.4679155,-21.191406,0.10980314064550523,-9.23186 +6f,20.753014483904757,0.081032848434397,6.401092992574548,0.07251730378843775,-7.383278,-21.735199,0.1087431923116869,-9.32958 +6b,20.13603647864346,0.07685946778401091,4.629126464261831,0.07240900796328872,-7.4767733,-22.983685,0.10559565437208587,-9.99707 +6e,20.230659191999795,0.07928690671596018,6.473428121372923,0.07344429925607286,-7.45753,-21.21476,0.10807626321168287,-9.40347 +6q,20.370202322296667,0.08170576695111131,5.510682288837353,0.07402045963744482,-7.511115,-22.370636,0.11024908524794168,-9.23883 +6n,24.866221114402183,0.07889585639482587,8.841178548761764,0.07270264783819581,-7.4860654,-23.51111,0.10728574536702304,-8.51749 +6l,24.51270039957944,0.08118281189247786,7.197506624747727,0.0735686807022225,-7.5833836,-24.89858,0.109558202463508,-10.4744 +6d,20.274280375409507,0.08055693646046642,6.009451652872728,0.07295789833552521,-7.3787923,-21.64362,0.10868429022371383,-8.48127 +6p,19.547777278799614,0.07969845352684161,5.952641640249409,0.07477379552003081,-7.497618,-21.092754,0.10928386885099517,-9.65303 +1,20.491271885714074,0.07927167792026477,5.069419520783191,0.07189171313496731,-7.5374126,-22.959267,0.10701596767667255,-9.72017 +6h,24.42242577675696,0.0779577887126581,5.739381555000283,0.07498379407439702,-7.400164,-26.083206,0.10816647444915185,-9.98459 +6i,24.034416594277072,0.08532528319548015,3.527903898023056,0.07612137382285822,-6.898845,-27.40536,0.1143453868989397,-10.2436 +11c,18.41441195765558,0.0823253350594936,3.168108629253317,0.07474558441655625,-7.450448,-22.696753,0.11119515808896728,-10.2066 +6o,27.162913749340102,0.08142153336406226,9.049137537732516,0.07508715955446645,-7.4556484,-25.569424,0.11075896182843628,-8.44621 +6m,22.626901631478194,0.08180138334060186,8.321926602390112,0.07615201713116627,-7.4214625,-21.726439,0.11176133512794816,-8.58909 +6j,21.26816444988208,0.08110220928068058,5.672567353227283,0.0753905871742157,-7.450614,-23.046211,0.11073079510542823,-8.87368 +6k,21.102728240851548,0.08292414662847213,7.211565812485795,0.07658508556797193,-7.419545,-21.310707,0.11287909206542161,-10.3039 +16,19.396684735244786,0.08224259495764104,3.166644918254823,0.07626904020142501,-7.4017406,-23.63178,0.11216421407299738,-11.2166 diff --git a/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/README.md b/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/README.md new file mode 100644 index 0000000..fad4dd5 --- /dev/null +++ b/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/README.md @@ -0,0 +1,33 @@ +# P2Y1 Ortho Sub + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 13.95 +- RMSE: 14.08 +- R²: 0.32 +- Kendall 𝜏: 0.32 +- Spearman ρ: 0.37 + +## System Details +- Ligands: 12 +- Host Atoms: 4820 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.79 Hours +- Average Time Per Molecule: 0.48 Hours +- Total Nanoseconds Simulated: 2189.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/dg_plot.png b/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/dg_plot.png new file mode 100644 index 0000000..4fdecfd Binary files /dev/null and b/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/dg_results.csv b/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/dg_results.csv new file mode 100644 index 0000000..71809b5 --- /dev/null +++ b/summaries/2026_jun_08_abfe/gpcrs/p2y1_ortho_sub/dg_results.csv @@ -0,0 +1,13 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +16,18.49666605731394,0.08303892236032419,2.842134960623493,0.07579081521764619,-7.449578,-23.104107,0.11242646618176405,-11.2166 +11b,16.87268529205256,0.07943223823860687,1.7026567072597563,0.0729227318695645,-7.777276,-22.947304,0.10782951958955951,-10.5657 +17,22.60655374349429,0.08195839567459978,1.7188562684849003,0.07771945373485518,-7.674436,-28.562134,0.11294906865662308,-11.0462 +14,21.22477727210832,0.08543882430767474,4.014877359696718,0.07595484665232914,-7.5109096,-24.720808,0.11431942717253507,-9.21816 +11e,19.003086112962215,0.07942294197452854,4.3798477339138735,0.0724324876392847,-7.4936337,-22.11687,0.10749171585524374,-9.70458 +11d,21.24513740285449,0.07832798870196939,2.884116141922218,0.07358525661007999,-7.816662,-26.177685,0.10747122314585966,-10.3039 +11f,16.56155788663191,0.07857545510170909,3.7057220132841797,0.07234410893291651,-7.8493204,-20.705158,0.10680717317548663,-9.22841 +18,18.560334440067447,0.08432132455605927,2.809331824771503,0.0780668589163439,-7.597559,-23.348562,0.1149109230489105,-11.1253 +12,20.5932691335714,0.08596331346936686,3.615424933535689,0.07549499511331016,-7.5043736,-24.482218,0.1144079785233152,-11.1253 +11a,19.68085267752921,0.07703905178296636,6.535916918881337,0.06980991698978516,-7.509472,-20.654408,0.10396364753960524,-7.774799999999999 +19,22.692008291254602,0.08158790720394256,3.65311681450802,0.07584426896496756,-7.57957,-26.618462,0.11139542062737355,-10.6355 +13,21.147481500745148,0.0812475491616645,2.355070653320897,0.07736461763865032,-7.572858,-26.365269,0.1121893413259551,-10.5033 diff --git a/summaries/2026_jun_08_abfe/jacs_set/bace/README.md b/summaries/2026_jun_08_abfe/jacs_set/bace/README.md new file mode 100644 index 0000000..09e1187 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/bace/README.md @@ -0,0 +1,33 @@ +# Bace + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 25.77 +- RMSE: 25.88 +- R²: 0.04 +- Kendall 𝜏: 0.12 +- Spearman ρ: 0.16 + +## System Details +- Ligands: 36 +- Host Atoms: 6101 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 18.81 Hours +- Average Time Per Molecule: 0.52 Hours +- Total Nanoseconds Simulated: 6527.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/bace/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/bace/dg_plot.png new file mode 100644 index 0000000..32ca1c5 Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/bace/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/bace/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/bace/dg_results.csv new file mode 100644 index 0000000..a110e16 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/bace/dg_results.csv @@ -0,0 +1,37 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CAT-13n,36.65788643621387,0.08203007934671622,14.601363459002345,0.07411151579466554,-7.5268054,-29.58333,0.11055067024225369,-8.543 +CAT-13e,40.326698533892454,0.08351111459169314,12.606832430493544,0.07315353289746225,-7.333151,-35.05302,0.11102047394839834,-9.963 +CAT-4a,42.7824023313154,0.08120364377703786,12.510417319869344,0.07480264441576266,-7.265551,-37.537537,0.11040592092029795,-7.933000000000001 +CAT-4m,44.05771189126043,0.08166287881078049,14.543700381538068,0.07401619852525244,-7.5606856,-37.074696,0.1102144428820189,-9.153 +CAT-17b,41.32902825786256,0.08419869224253983,14.060297993194155,0.074096926468645,-7.7475934,-35.016323,0.11215959293548511,-10.023 +CAT-13j,39.88442765650175,0.08298875556431033,10.989693626945128,0.07525455350700097,-7.4971848,-36.39192,0.11202848465301546,-8.733 +CAT-13d,43.63460986528489,0.07791913849481373,13.818559853242027,0.072030197655442,-7.4726944,-37.288746,0.10611192919769202,-10.473 +CAT-13b,42.047330788463704,0.07822028660971089,14.66970303018832,0.07254364903041728,-7.489631,-34.867256,0.1066817428239419,-9.123 +CAT-13a,44.180063101605505,0.0762789374665002,15.540262628947284,0.07049685158752675,-7.323964,-35.96376,0.10386665675168341,-8.843 +CAT-13h,38.75082855723826,0.07969503268808178,12.273199819672096,0.07294578151587448,-7.483275,-33.960907,0.10803881374819015,-9.633 +CAT-13o,34.830198470283676,0.07940153738229058,12.968014308393785,0.07388803607053025,-7.5683527,-29.430536,0.10846218701939984,-8.543 +CAT-13g,38.52269209900098,0.08241268776620787,11.391271851401033,0.07442338600831885,-7.506049,-34.637466,0.11104364677816422,-9.093 +CAT-4k,44.734116850662524,0.07977154432655978,16.147303845640227,0.07396168990490815,-7.009083,-35.595894,0.10878341260428487,-7.853 +CAT-17g,47.246058040017296,0.08147793060659367,16.47928781556057,0.0742309457211191,-7.4470367,-38.213806,0.11022198727379498,-9.743 +CAT-4l,42.22793853558178,0.08209324885468657,18.324483221643064,0.07346758389890888,-7.2725997,-31.176054,0.11016708851313406,-9.343 +CAT-4j,42.47924472920199,0.07988773180351044,16.106508769285156,0.07553360433611617,-7.462581,-33.835316,0.1099425990083669,-9.023 +CAT-4n,48.22291357509562,0.08133114208594522,18.645921116817167,0.07556441053847425,-7.4630017,-37.039997,0.11101682220740822,-9.093 +CAT-13i,43.54084790467539,0.08032570016676992,12.085094375088433,0.07536438109439351,-7.492365,-38.948116,0.11014539502413526,-9.273 +CAT-17f,44.46729043455477,0.08307873291760136,19.549128954059693,0.07391076173911668,-7.857217,-32.775383,0.11119746653611588,-9.423 +CAT-4p,43.41948349102476,0.08196336188918937,15.274717367729517,0.0753511405784484,-7.292212,-35.436977,0.11133636907431153,-10.083 +CAT-13c,39.98021834028124,0.08157836218855233,13.2407659379251,0.07278430827607282,-7.2933598,-34.03281,0.10932787708811063,-9.323 +CAT-24,48.17796985694267,0.0817599972887315,16.189815010861587,0.0743443985713201,-7.655297,-39.64345,0.11050695342640064,-11.35 +CAT-4i,38.94872441407011,0.08238810187714819,14.799051068374503,0.07340405712003234,-7.5686593,-31.718328,0.11034470958138555,-8.263 +CAT-4c,44.179220227868896,0.0832137382187216,13.045068287207176,0.07741179319051368,-7.675449,-38.8096,0.1136534731246907,-7.853 +CAT-17i,46.70753466589744,0.07922560344720127,16.267618840595077,0.07577904621204393,-7.6735024,-38.113422,0.1096319300495083,-9.473 +CAT-13k,44.788678997077675,0.08174261802612408,16.695651748517555,0.07488135012088949,-7.4100904,-35.503117,0.11085608777912045,-9.703 +CAT-17a,43.91110003249286,0.07835168732519131,13.37803027322627,0.07337571916277892,-7.283232,-37.8163,0.10734515857438354,-10.733 +CAT-17c,45.69134765859183,0.08054229959753302,16.821441003527745,0.0750610942887431,-7.6278915,-36.4978,0.11009645725581886,-9.863 +CAT-4o,41.10582564704927,0.08106918678380859,14.812411945992116,0.0736974165220858,-7.491578,-33.78499,0.10956058710968032,-9.383 +CAT-17d,43.36958816150467,0.07951926679059035,17.251588662053543,0.07220630481623805,-7.4575357,-33.575535,0.10741072686714567,-9.423 +CAT-4b,38.23136950509001,0.08331722178397961,12.988134866390826,0.07490827620330037,-7.728747,-32.97198,0.11204021282356966,-9.633 +CAT-13f,38.47104358971513,0.08422303381411268,12.10327016417452,0.07625776243796407,-7.5081706,-33.875942,0.11361674945578285,-9.093 +CAT-4d,42.770874821655184,0.08445898111566574,12.571777310228725,0.07754677566317739,-7.226661,-37.425762,0.11465959142981255,-9.113 +CAT-13m,45.2080861450374,0.08230340209681651,18.68578592960538,0.07432298778499481,-7.330619,-33.85292,0.11089525016879104,-8.763 +CAT-17h,40.69983416771597,0.08073383672177739,16.437119731444835,0.07310111859493697,-7.326662,-31.589376,0.10891155095603795,-10.333 +CAT-17e,43.89108313392824,0.08094486181198343,16.990726646622974,0.07597374733262101,-7.835369,-34.735725,0.11101387722947989,-10.023 diff --git a/summaries/2026_jun_08_abfe/jacs_set/cdk2/README.md b/summaries/2026_jun_08_abfe/jacs_set/cdk2/README.md new file mode 100644 index 0000000..6700598 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/cdk2/README.md @@ -0,0 +1,33 @@ +# Cdk2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 22.06 +- RMSE: 22.21 +- R²: 0.21 +- Kendall 𝜏: 0.30 +- Spearman ρ: 0.34 + +## System Details +- Ligands: 16 +- Host Atoms: 9028 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 10.91 Hours +- Average Time Per Molecule: 0.68 Hours +- Total Nanoseconds Simulated: 2899.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/cdk2/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/cdk2/dg_plot.png new file mode 100644 index 0000000..15f36ee Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/cdk2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/cdk2/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/cdk2/dg_results.csv new file mode 100644 index 0000000..eac41d6 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/cdk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,28.471655005700804,0.07859035679280411,8.620043013097133,0.07421848409515383,-7.13697,-26.98858,0.10809638089317725,-7.04 +28,49.87274006726127,0.08481709618957078,23.57900735856083,0.07803768823118722,-7.2146554,-33.50839,0.11525545796403257,-11.11 +22,27.192484276226956,0.07888589804634373,8.435089233862282,0.0748793638121674,-7.33348,-26.090876,0.1087653622965191,-7.86 +30,43.320780560966554,0.08259147071901526,18.76192880728482,0.07692214089947015,-7.0785813,-31.637436,0.11286437345809304,-9.81 +1h1r,32.97660215698528,0.07802678202772446,8.278869383431722,0.0726431954383376,-7.1194305,-31.817163,0.1066077509240981,-7.669999999999999 +1h1s,51.33180308742014,0.08268592993609201,26.918920508737287,0.07650594113555509,-7.2275033,-31.640383,0.11265044180309876,-11.25 +21,35.11425328090883,0.07786630863214707,10.288552642853885,0.07621176678281266,-7.11112,-31.936821,0.10895593336828704,-7.829999999999999 +1oiy,43.81580503353691,0.08076962623777037,18.117160715035414,0.07343404676182466,-7.0998616,-32.798508,0.10916176870318187,-9.79 +1oiu,52.463974577624995,0.08284065209766688,26.741596229237544,0.07782970429727079,-7.1708922,-32.893265,0.11366633851306768,-9.08 +31,35.98289946021435,0.0863102104432825,15.670075486730816,0.0758681901328497,-7.18457,-27.497393,0.11491490199620737,-9.54 +29,43.44348347199496,0.08328049178258927,19.58273397931032,0.07739986952541116,-7.127399,-30.988146,0.11369423958187412,-9.88 +26,35.3524447015486,0.07871676228974157,10.482475457717856,0.07475631415842839,-7.1540823,-32.02405,0.10855798069203997,-8.43 +1oi9,39.007218400778065,0.0802041250410082,15.199481125114298,0.07489138862808395,-7.155394,-30.96313,0.10973341225094743,-9.74 +20,39.13762912625626,0.08012946236484597,13.611488201619313,0.07527983979700772,-7.1490655,-32.67521,0.10994446333828009,-8.72 +32,56.39147344719695,0.08123974734881761,25.421883074626827,0.07833559124546718,-7.184672,-38.154263,0.11285548903388187,-9.75 +1h1q,29.587503587888975,0.07728403456188773,9.73357030303173,0.07207635927119352,-7.117084,-26.971016,0.10567792373032894,-8.18 diff --git a/summaries/2026_jun_08_abfe/jacs_set/jnk1/README.md b/summaries/2026_jun_08_abfe/jacs_set/jnk1/README.md new file mode 100644 index 0000000..d3ec413 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/jnk1/README.md @@ -0,0 +1,33 @@ +# Jnk1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 25.67 +- RMSE: 25.80 +- R²: 0.09 +- Kendall 𝜏: 0.22 +- Spearman ρ: 0.35 + +## System Details +- Ligands: 21 +- Host Atoms: 5993 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 9.81 Hours +- Average Time Per Molecule: 0.47 Hours +- Total Nanoseconds Simulated: 3703.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/jnk1/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/jnk1/dg_plot.png new file mode 100644 index 0000000..b80c351 Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/jnk1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/jnk1/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/jnk1/dg_results.csv new file mode 100644 index 0000000..e114a54 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/jnk1/dg_results.csv @@ -0,0 +1,22 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +18626-1,37.64292123483935,0.07429656157718377,9.237486689618878,0.0701452292962783,-7.1734056,-35.578842,0.10217794407414801,-8.87 +18628-1_flip,36.9900284395472,0.07558871557313308,8.608480545755754,0.07157406872138185,-7.1417913,-35.52334,0.10409851696988341,-8.7 +18629-1,37.188076638473206,0.07429849526531197,9.063861727911913,0.07229547715516316,-7.1381173,-35.26233,0.1036672678128555,-8.67 +18636-1,38.427596690971704,0.07570344481964783,8.521771717929674,0.07229422212866947,-7.191966,-37.097794,0.10467791606041299,-7.51 +17124-1,42.203708862364685,0.07766306475426708,8.927572092372175,0.07408696550129817,-7.160661,-40.4368,0.1073332664378385,-9.68 +18627-1,34.02945705087269,0.07424746448827578,9.648288326838728,0.07343085429518309,-7.2249737,-31.606142,0.1044259371299017,-8.48 +18638-1,48.03255322771922,0.07985454379284485,16.84095132912404,0.07744504142594766,-7.0963697,-38.28797,0.11124065176827276,-10.09 +18659-1,39.58971181529797,0.0782409647607707,9.683177858545823,0.07559425862132262,-7.17861,-37.085144,0.10879402788390351,-9.47 +18639-1,39.05932362503094,0.07988948938418888,9.728260154714679,0.07618366557469385,-7.1815634,-36.512627,0.11039149158546244,-9.74 +18634-1,34.83599396297198,0.07771287319244549,7.7130582534039185,0.07374275092236224,-7.179543,-34.302475,0.10713208657271019,-9.99 +18630-1,33.3530759692687,0.0762807934164939,8.857540493614048,0.07235565536772252,-7.1016364,-31.59717,0.10513848157521798,-9.14 +18637-1,43.20774766325423,0.07937169235748559,13.550430928283227,0.07815256040389253,-6.782072,-36.43939,0.11138980314811317,-10.14 +18658-1,37.18194738152775,0.07809095608653248,10.528221201993416,0.07509134724005985,-7.2243776,-33.878105,0.10833701054042422,-9.7 +18632-1,36.04154400342348,0.07676059688026678,10.472489646175996,0.07223491850920333,-7.1176796,-32.686733,0.10540432953843056,-9.08 +18633-1,33.030886074850514,0.07649446033663417,10.37869620356094,0.07228799375717941,-7.013462,-29.665653,0.10524712111801875,-9.17 +18635-1,33.84681553031724,0.08025186388607598,7.617587497279444,0.07344379679586273,-7.266049,-33.49528,0.10878581224121665,-7.29 +18631-1,32.91605785272011,0.07713911794304548,8.970078524885734,0.0726976218910605,-7.087283,-31.033262,0.1059971119684243,-9.41 +18660-1,44.90546173484018,0.08355634690839454,15.239081053678122,0.07756393703232822,-7.2056417,-36.87202,0.11400801479120208,-8.7 +18625-1,36.15838159544446,0.0733398187400361,8.991473027564139,0.07064146813558334,-7.1450734,-34.311985,0.10182802184650346,-8.11 +18624-1,33.61782658208097,0.07785890194382643,10.027077809455777,0.07177614875591867,-7.2017245,-30.792473,0.10589534523353773,-8.49 +18652-1,45.981385780314824,0.08500636913686378,15.49698477051557,0.07903165193820716,-7.227288,-37.71169,0.1160693103361723,-10.68 diff --git a/summaries/2026_jun_08_abfe/jacs_set/mcl1/README.md b/summaries/2026_jun_08_abfe/jacs_set/mcl1/README.md new file mode 100644 index 0000000..c5eb072 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/mcl1/README.md @@ -0,0 +1,33 @@ +# Mcl1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.36 +- RMSE: 21.54 +- R²: 0.09 +- Kendall 𝜏: 0.14 +- Spearman ρ: 0.23 + +## System Details +- Ligands: 42 +- Host Atoms: 2542 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 16.78 Hours +- Average Time Per Molecule: 0.40 Hours +- Total Nanoseconds Simulated: 7813.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/mcl1/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/mcl1/dg_plot.png new file mode 100644 index 0000000..72b7943 Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/mcl1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/mcl1/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/mcl1/dg_results.csv new file mode 100644 index 0000000..4eb5112 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/mcl1/dg_results.csv @@ -0,0 +1,43 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +23,77.17149587037729,0.08063100105063647,55.127214049206664,0.07695732083747021,-7.152662,-29.196938,0.11146204538276278,-8.83 +26,78.54979759640474,0.0804402835580384,53.57386026872135,0.07662724004923838,-7.239026,-32.214962,0.11109623367360939,-8.24 +27,73.57618019834497,0.08479998215022842,56.41735935759143,0.07534881038021954,-7.3454533,-24.504272,0.11343932386255366,-6.12 +28,73.97430783831098,0.08655672189213785,55.22137951349318,0.07587127334416183,-7.0467277,-25.799662,0.11510219903884293,-6.62 +29,70.08759695041502,0.08651803189786952,53.14414757061456,0.0756509646354186,-6.977418,-23.920862,0.11492797002362011,-6.94 +30 flip,72.8585234439563,0.08282287612766134,55.33469865041484,0.07375923724952595,-6.9319468,-24.455769,0.1109056080173126,-7.85 +31,73.0914298456922,0.0884073837060467,52.12379509840191,0.07714756656115289,-6.8794885,-27.847126,0.11733546999972211,-7.920000000000001 +32,74.55939138774225,0.08033609557703997,55.63067981486945,0.07500101842361871,-7.269691,-26.1984,0.10990469060573936,-6.58 +33,79.52781369225305,0.07760452693755177,54.77969456278648,0.07543527105577008,-6.982582,-31.730703,0.10822634947395528,-6.88 +34,77.51434162286712,0.08056960816924454,52.4053039052253,0.0773092075137213,-7.2108736,-32.31991,0.11166098390639954,-6.87 +35,75.13301752213832,0.08460999096560629,53.37554206273622,0.07580882065221037,-7.183235,-28.940708,0.11360381974158693,-8.81 +36,76.0031936921445,0.07964388954101172,52.76199000617279,0.07769327574153806,-7.7032895,-30.944496,0.11126272617849853,-8.18 +37,77.26682229089829,0.08098260181900072,52.725405999715086,0.07744851378060214,-7.641931,-32.18335,0.1120555847970057,-8.95 +38 flip,80.81787022169539,0.08263328579543534,55.458619082251985,0.07812795158295804,-7.0250483,-32.384296,0.11371999270092806,-7.02 +39,78.81048535725569,0.08378645968630348,55.84690090605186,0.07920135461574442,-6.8317566,-29.795341,0.11529538325420258,-7.03 +40 flip,76.49365366592863,0.0822107814954033,53.851701686590445,0.07925298435889339,-7.505354,-30.147305,0.11419127866818876,-7.25 +41 flip,75.76000146576278,0.08473684853469687,53.744071016373304,0.0803260401446295,-6.909439,-28.925373,0.11675875224114375,-7.13 +42,78.43840364489441,0.08128737344576045,55.945667297111854,0.07445142282920075,-7.514052,-30.006784,0.11022999339110458,-8.9 +43 flip,81.1407663243873,0.07766245093597207,56.411345536892455,0.07724094893910524,-7.475944,-32.20537,0.10953364998207506,-7.03 +44,79.21899615069151,0.09016827337316222,53.75303465742744,0.07817880968340944,-7.1882825,-32.654243,0.11934087232215151,-8.67 +45,76.37362919745327,0.08260811363406363,54.67194386502588,0.07612944234752424,-7.3398304,-29.041515,0.11233784950017241,-8.95 +46 flip,79.55267543757786,0.1096397850730729,55.405788593833336,0.07630461163440147,-6.8938675,-31.040749,0.13357872670281917,-7.6 +47 flip,78.67721732105176,0.0839148699818977,57.2456531055506,0.0761437877251732,-7.47632,-28.907885,0.11331187851772219,-5.78 +48 flip,77.7295370279823,0.07968370107612298,60.989836392860575,0.075446706693009,-6.9968743,-23.736582,0.10973466985419808,-6.66 +49,77.47086900633352,0.0774346314287514,50.32184780087181,0.07584170854976278,-7.4040246,-34.55305,0.10838859211307125,-8.36 +50,69.54161265464009,0.0977562071159058,49.07017419472052,0.07777990675523129,-7.6908636,-28.162302,0.12492393655557105,-9.33 +51,72.65248806008258,0.08424874855796954,52.65968231148799,0.07604923382008645,-7.736939,-27.729746,0.11349598053766555,-8.45 +52,69.40752540632431,0.0805778890560287,50.05885057094132,0.07657172426186068,-6.99548,-26.344152,0.11115765903058634,-9.23 +53,76.53536412422005,0.08048186124028638,49.936150752104496,0.07733954580370869,-6.9758124,-33.575024,0.11161870512519247,-9.96 +54,75.24928486413343,0.08129533791543515,52.836386041937104,0.07581188378226662,-6.8269515,-29.239851,0.11115922673984689,-9.78 +56,71.394749071872,0.08573290140078123,51.90044014461716,0.0782850659602598,-6.8077946,-26.302107,0.1160977257959789,-9.26 +57,76.99527807033382,0.0802642284832102,55.58164939268842,0.07774793052732808,-7.3265934,-28.740229,0.1117456355983857,-9.04 +58,75.60440884751114,0.08633445391159862,48.78476610559347,0.07892950230011692,-7.6730914,-34.492737,0.11697651159766266,-9.41 +60,70.94499173992632,0.08297685982523834,52.090874349906976,0.0751958240544806,-7.1933722,-26.04749,0.11198022692283514,-8.92 +61,72.45681492577276,0.08691732852919008,48.572361019208124,0.07723506497059641,-7.1190677,-31.003521,0.11627500702929848,-8.08 +62,71.32222683261912,0.08158551063510326,51.258287476040245,0.07632900319527915,-7.835744,-27.899685,0.11172426895878747,-7.959999999999999 +63,76.3830089803214,0.08580119580132639,48.79621774877409,0.07600623338735653,-6.8803406,-34.467136,0.11462457290943709,-9.06 +64,76.25097323434974,0.0807700764768369,52.10809313860554,0.07834239778905135,-6.831314,-30.97419,0.11252260459752982,-9.5 +65,71.76327974062802,0.08381070225935477,48.92539345068429,0.07646239809257079,-6.918612,-29.756502,0.11344924916134522,-8.41 +66,73.24878973852043,0.07937424459522832,52.02938633463409,0.07587556536668856,-7.4041934,-28.6236,0.10980606597441582,-8.43 +67,72.78247548229506,0.0824651376266744,49.86582849044733,0.07705691813965185,-7.8233852,-30.74003,0.11286393381841409,-7.58 +68,71.53492366784441,0.08597726287787032,50.01842494073913,0.07816072875782869,-7.229256,-28.745752,0.11619461799896451,-7.690000000000001 diff --git a/summaries/2026_jun_08_abfe/jacs_set/p38/README.md b/summaries/2026_jun_08_abfe/jacs_set/p38/README.md new file mode 100644 index 0000000..22d4779 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/p38/README.md @@ -0,0 +1,33 @@ +# P38 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 25.76 +- RMSE: 25.83 +- R²: 0.57 +- Kendall 𝜏: 0.53 +- Spearman ρ: 0.72 + +## System Details +- Ligands: 34 +- Host Atoms: 6680 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 25.62 Hours +- Average Time Per Molecule: 0.75 Hours +- Total Nanoseconds Simulated: 6078.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/p38/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/p38/dg_plot.png new file mode 100644 index 0000000..e996b2a Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/p38/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/p38/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/p38/dg_results.csv new file mode 100644 index 0000000..41d6e7e --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/p38/dg_results.csv @@ -0,0 +1,35 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2j,35.483841599997966,0.08198183825677885,6.599547642242132,0.07442199508525572,-7.367773,-36.252068,0.11072332706539517,-10.08 +2gg,47.56095060970446,0.08363071017781235,17.80182868322011,0.07545938511247918,-6.941785,-36.70091,0.11264197479802407,-10.66 +2q,48.3209128271991,0.0873659079257556,14.460564681051375,0.07873695903548375,-6.8286867,-40.689034,0.11761084382762947,-12.26 +2t,41.05515399374874,0.08047433736895693,10.006798623761597,0.07576801362616745,-7.403968,-38.452324,0.11053013554604822,-11.85 +2g,40.483365486459846,0.07825648615114249,10.21041617488297,0.07263726116327429,-6.8307223,-37.103672,0.10677195012748279,-10.66 +2l,38.27257899317434,0.07914917542197865,7.129799764273928,0.07450564952536493,-7.459162,-38.601944,0.1086999713945485,-12.26 +2ee,44.06971906558641,0.08278164344168328,12.934278311419824,0.07868644590855892,-6.934435,-38.069878,0.11421189631831945,-12.26 +2aa,38.93886904929951,0.07597209352407738,12.718442441000517,0.07363179588529922,-6.884538,-33.104965,0.10579886747846372,-9.27 +2o,49.413927930490715,0.08067344791194947,15.779863377526295,0.07913618946263451,-6.8668165,-40.50088,0.11300770628885452,-10.49 +3flw,42.917656645300134,0.08213592138981828,13.754652955409567,0.07606932268510724,-6.8954945,-36.0585,0.11195021856309785,-10.68 +2u,54.1601921086779,0.08776585057868345,20.503794087693517,0.08102445732150103,-7.302494,-40.958893,0.11944792678001379,-12.26 +2p,47.906522216249314,0.08384648559240307,15.11692801454941,0.0789427880798019,-6.830467,-39.620064,0.11516161224995752,-11.2 +2h,33.31485120571481,0.07798542579608254,8.439010289891526,0.07476138344373344,-6.8068447,-31.682688,0.10803236131371578,-9.48 +3fmk,41.412323799152894,0.07733354181057596,9.444535755623084,0.07376961688065523,-6.9290767,-38.896862,0.10687578333601469,-11.83 +2i,34.543237039100774,0.0794963000111393,7.559441265827474,0.0718758073728038,-7.611778,-34.595573,0.10717179386831903,-10.05 +2f,34.83099624025289,0.07888958725398021,8.475585739374036,0.07212196061292543,-6.8050723,-33.160484,0.10688846607448217,-8.48 +2x,39.70528306045794,0.07777072347359495,9.595949411780179,0.07248155511031884,-6.8683186,-36.977654,0.1063102124013331,-10.23 +2ff,40.63537300217953,0.07879696714256851,11.941892486513899,0.07607634275934967,-6.8242598,-35.517742,0.10952886358629435,-11.44 +2k,40.862364018377875,0.07894786173480316,11.261715816968477,0.0726258647434598,-7.444179,-37.044823,0.10727199589004073,-10.55 +2n,42.378510946229326,0.08037921677866268,9.694963758482414,0.07623946216877779,-6.8567777,-39.54033,0.11078480979690197,-11.85 +3flq,43.14356995869146,0.08369431743835903,14.9129194132954,0.07688280440076191,-6.9176216,-35.14827,0.11364728058338494,-9.93 +3fln,37.266246596499066,0.07842803426056062,8.424354993865027,0.07292757514234179,-6.8094926,-35.651386,0.10709522759730042,-10.88 +2e,37.64813862325564,0.07564410585659047,8.7723417291841,0.07413699420073985,-6.8497515,-35.725548,0.1059165929397448,-10.7 +3fmh,41.914915402387166,0.07787631590062019,9.79777290456114,0.07341673944596348,-6.940658,-39.057804,0.10702681070241082,-10.83 +2c,39.57115838779201,0.07686966473209213,8.941433827759564,0.07357124837740923,-7.466974,-38.096695,0.10640335494633,-10.46 +2y,38.86158208069125,0.07919446509637525,10.442867105725743,0.07409653217412941,-6.9374003,-35.356117,0.10845302845994109,-9.78 +2s,41.31768151019528,0.08193951315768776,12.028755112679665,0.07765891964258564,-7.3952336,-36.684162,0.11289371823344493,-11.11 +2m,36.917419317709474,0.08158839124451761,7.844400124249586,0.07420037492906587,-7.4982038,-36.57122,0.11028309582833819,-10.96 +2bb,40.07136659299817,0.08066413774034471,17.099959485476507,0.07528704867939119,-6.7877192,-29.759125,0.11033967018369378,-9.06 +2v,37.044693340570575,0.07457704254706526,9.913632165889606,0.07059923464411116,-7.4026055,-34.533665,0.10269365709429695,-8.97 +2r,34.247368528514734,0.08330407405427988,7.944929756829306,0.07678670545271507,-6.803935,-33.106373,0.11329504352937496,-10.79 +3flz,37.404018549845595,0.07891122246844187,9.544950956603936,0.07394759963722154,-6.8425236,-34.70159,0.1081444798571371,-9.49 +2z,37.116148264516724,0.07965577623582429,9.369209053430062,0.07458536493846138,-6.8000035,-34.54694,0.10912387158974508,-10.36 +3fly,36.374807248437754,0.0754108597171898,7.325664750152835,0.07360999107912405,-6.958427,-36.00757,0.1053813482071396,-11.42 diff --git a/summaries/2026_jun_08_abfe/jacs_set/ptp1b/README.md b/summaries/2026_jun_08_abfe/jacs_set/ptp1b/README.md new file mode 100644 index 0000000..0bed35c --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/ptp1b/README.md @@ -0,0 +1,33 @@ +# Ptp1B + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 19.85 +- RMSE: 20.13 +- R²: 0.42 +- Kendall 𝜏: 0.44 +- Spearman ρ: 0.60 + +## System Details +- Ligands: 23 +- Host Atoms: 5488 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 13.20 Hours +- Average Time Per Molecule: 0.57 Hours +- Total Nanoseconds Simulated: 4972.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/ptp1b/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/ptp1b/dg_plot.png new file mode 100644 index 0000000..eb5b701 Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/ptp1b/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/ptp1b/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/ptp1b/dg_results.csv new file mode 100644 index 0000000..a62d289 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/ptp1b/dg_results.csv @@ -0,0 +1,24 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +23477,166.79660336315627,0.08541375020542614,143.02284777946585,0.08246114807190796,-6.98483,-30.758596,0.11872383781487215,-8.85 +23484,170.73269867036328,0.09947645954058493,147.36077860350838,0.08953486831998256,-6.8281612,-30.200075,0.13383593929810575,-7.75 +23467,152.80941907104656,0.08456899295737219,138.93080117147383,0.0809680191082277,-7.1564503,-21.035057,0.11708003539517059,-7.34 +20667,177.96426349083688,0.09722884380123738,150.1354681242583,0.09054616926936894,-6.8262186,-34.655014,0.13286104333581994,-11.42 +23469,167.15261717171734,0.09150431335625053,145.36119208003575,0.08504983872377689,-7.1945825,-28.98601,0.12492603583616728,-7.72 +23483,177.93510328126004,0.09390444811182164,154.68120453352032,0.08851212523939153,-7.097306,-30.351204,0.12904434001373144,-9.87 +23480,170.96866933948147,0.09118512207176165,145.0384630234889,0.08587548775015982,-7.149477,-33.07967,0.12525703925755996,-8.72 +23474,164.8296827834491,0.09171069789297806,140.0744572566897,0.0859245432592975,-7.0587482,-31.813976,0.12567370147463622,-9.11 +23473,162.27815845570458,0.08903341013875882,137.67142087650862,0.08327556852531562,-7.2755933,-31.882336,0.121908852976931,-8.39 +23471,166.35782139970073,0.08985755760706429,144.65143047792063,0.08107157513768172,-7.3794093,-29.085804,0.12102471216413468,-7.75 +20669,155.86361329883553,0.08940419133970111,142.07324062402412,0.0844988926628229,-7.225006,-21.015379,0.12301695936068796,-8.61 +23476,162.30292249920694,0.09109721103228394,140.03454355192497,0.08410000219823713,-7.3307486,-29.599133,0.12398190282296835,-9.41 +23466,161.33977640650937,0.08568470125472265,145.0795224795313,0.08054762288886576,-7.2194624,-23.47973,0.11760011727102146,-7.85 +23472,168.26466433708077,0.09106362401186002,146.58462419952198,0.08612602853085959,-7.19776,-28.877798,0.12534064148819346,-8.65 +23482,178.26015674270485,0.09165676800561741,152.61487572239952,0.08663885470632751,-7.2395806,-32.884865,0.12612396388497982,-10.01 +23486,181.5173933767464,0.0970633681744698,152.332149882155,0.09107693587138635,-6.8227983,-36.00803,0.1331026133819066,-12.47 +23470,162.07189919503136,0.09293438554149436,145.62539666322652,0.08484394481162899,-7.153131,-23.599644,0.12583836850171676,-7.72 +23468,162.82978300903633,0.08985449200732638,146.50137643503555,0.08393588254288767,-7.2687,-23.597105,0.12295959544561018,-7.75 +23485,178.69944829965834,0.09550426093220053,154.52105216129917,0.08871602855548338,-6.815609,-30.994,0.13035182230741227,-11.01 +23330,157.01678283052206,0.09396813760284048,137.47981633290945,0.0897462765422747,-7.0826206,-26.61957,0.1299400055323564,-10.13 +20670,164.9371251726392,0.0874329155210767,141.4096913355825,0.08360342875856058,-7.2641387,-30.791565,0.12097126938535217,-9.08 +23479,167.57627123151778,0.0922041439929238,146.7516132719672,0.08728787256539444,-7.2451367,-28.069798,0.12696762133103215,-9.14 +23475,160.94255654676334,0.08804389412234041,141.4750353944528,0.08436186995862008,-7.233377,-26.70091,0.12193708375691546,-8.72 diff --git a/summaries/2026_jun_08_abfe/jacs_set/thrombin/README.md b/summaries/2026_jun_08_abfe/jacs_set/thrombin/README.md new file mode 100644 index 0000000..aeef275 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/thrombin/README.md @@ -0,0 +1,33 @@ +# Thrombin + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 26.53 +- RMSE: 26.61 +- R²: 0.02 +- Kendall 𝜏: -0.16 +- Spearman ρ: -0.13 + +## System Details +- Ligands: 11 +- Host Atoms: 5256 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 5.27 Hours +- Average Time Per Molecule: 0.48 Hours +- Total Nanoseconds Simulated: 2129.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/thrombin/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/thrombin/dg_plot.png new file mode 100644 index 0000000..d0e6a2e Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/thrombin/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/thrombin/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/thrombin/dg_results.csv new file mode 100644 index 0000000..e77c0f1 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/thrombin/dg_results.csv @@ -0,0 +1,12 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +6a,45.53542692718826,0.0835257185837391,17.409091651721997,0.07836691690512598,-7.3945346,-35.52087,0.11453348562819915,-9.18 +3a,42.91248125521469,0.08445082121330863,16.08740632110046,0.07596201613295826,-7.351901,-34.17698,0.11358771543871296,-8.32 +1d,44.77166120546668,0.08289638800826035,17.62401956968271,0.07834100074152055,-7.36116,-34.5088,0.11405754487099472,-8.25 +6e,44.03847468213877,0.08367481554855655,18.14357213565483,0.07620015900148248,-7.33184,-33.22674,0.11317216525690481,-8.91 +6b,44.02071611046976,0.0857878235509692,16.84989642412837,0.07974994763040638,-7.2173905,-34.388206,0.11713071679395114,-8.89 +1b,45.542763158594674,0.08241585164897759,17.794878238840443,0.07732115283512407,-7.4484415,-35.196323,0.11300855400711443,-8.46 +1a,46.502242223667736,0.08667302751393101,18.055965077394717,0.07695085432213862,-7.070044,-35.516323,0.11590361374580882,-7.48 +5,43.06227179742207,0.08404948983562072,18.19674272902037,0.07837193004733016,-6.9752398,-31.840767,0.1149194333477664,-7.58 +3b,47.8872977385636,0.08770893363743991,15.275455518382492,0.08017395085536337,-7.371679,-39.983524,0.11883063340559563,-7.86 +7a,42.82758476820435,0.0859818777749511,15.517774385605383,0.07746346055614182,-7.430462,-34.740273,0.11573016472398011,-8.22 +1c,44.97843717349881,0.08387423986804042,17.76453343541635,0.07678199393196847,-7.2013426,-34.41524,0.11371175271540943,-8.56 diff --git a/summaries/2026_jun_08_abfe/jacs_set/tyk2/README.md b/summaries/2026_jun_08_abfe/jacs_set/tyk2/README.md new file mode 100644 index 0000000..a042e3c --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/tyk2/README.md @@ -0,0 +1,33 @@ +# Tyk2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 20.83 +- RMSE: 20.96 +- R²: 0.08 +- Kendall 𝜏: 0.15 +- Spearman ρ: 0.21 + +## System Details +- Ligands: 16 +- Host Atoms: 4670 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.61 Hours +- Average Time Per Molecule: 0.41 Hours +- Total Nanoseconds Simulated: 2677.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/jacs_set/tyk2/dg_plot.png b/summaries/2026_jun_08_abfe/jacs_set/tyk2/dg_plot.png new file mode 100644 index 0000000..6a39869 Binary files /dev/null and b/summaries/2026_jun_08_abfe/jacs_set/tyk2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/jacs_set/tyk2/dg_results.csv b/summaries/2026_jun_08_abfe/jacs_set/tyk2/dg_results.csv new file mode 100644 index 0000000..add1be4 --- /dev/null +++ b/summaries/2026_jun_08_abfe/jacs_set/tyk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +jmc_23,34.792504400956524,0.07242968578128092,8.300665413774128,0.07278507425660423,-6.9834013,-33.475243,0.10268264905481586,-11.7 +ejm_47,28.05098143571841,0.07692377029573458,7.525033045718291,0.07276099476821396,-6.9081545,-27.434103,0.10588403466137374,-9.7 +ejm_49,26.952876645565645,0.0783311263713217,8.601877632108312,0.0734951926822788,-6.9823413,-25.33334,0.10741186482882259,-7.75 +ejm_31,32.84116633605339,0.07204973515772738,8.961381061273956,0.0679417489942248,-6.879535,-30.759323,0.09903153837385796,-9.54 +ejm_45,33.430984319047646,0.07397431246264437,9.861202288518559,0.07154855420730788,-6.9464073,-30.51619,0.10291450098735852,-9.56 +ejm_44,31.55879019118599,0.07773350601915327,5.357394787102619,0.07224250226724048,-6.900498,-33.101894,0.10612010691599394,-7.42 +ejm_43,31.000649400140137,0.07660314506181441,6.761961143444126,0.07035926401799374,-6.8886967,-31.127382,0.10401186406614935,-8.26 +ejm_50,32.88234962601757,0.07357458665354792,12.392230726372748,0.07171191932416222,-6.919262,-27.409384,0.1027415163134922,-8.98 +ejm_42,30.62520893895771,0.07138685873095098,7.8451880256011775,0.06999154763682541,-6.967287,-29.747309,0.09997449844870818,-9.78 +ejm_55,33.7614358325505,0.07112743767337851,7.384520015777579,0.06924550933598192,-6.954614,-33.33153,0.09926758258958411,-9.21 +ejm_48,31.6685348166123,0.07690085389678569,6.787113126239986,0.07237120539987126,-7.032097,-31.913517,0.1055998707436952,-9.0 +ejm_54,33.10848426789147,0.07569598642945169,10.268890761502835,0.0725090655396031,-6.9562206,-29.795813,0.10482102340157815,-10.53 +jmc_28,31.082578039334084,0.07655024484182076,6.617629144472997,0.07261373672498234,-6.949138,-31.414087,0.10551158584017091,-10.98 +jmc_27,29.76883758526803,0.07465031921182778,7.740646970292267,0.071414688509297,-6.9454618,-28.97365,0.1033088955187679,-11.28 +jmc_30,37.335862944436144,0.07525983031236361,11.752769999401563,0.07322466178694675,-6.97983,-32.562927,0.10500425302081105,-10.94 +ejm_46,32.695834674313815,0.0763329329379358,7.2763222735776365,0.06988329056743735,-6.9359856,-32.3555,0.10349101869940347,-11.31 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/README.md b/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/README.md new file mode 100644 index 0000000..1cd0b9c --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/README.md @@ -0,0 +1,33 @@ +# Bace Ciordia Prospective + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 28.03 +- RMSE: 28.15 +- R²: 0.39 +- Kendall 𝜏: 0.39 +- Spearman ρ: 0.55 + +## System Details +- Ligands: 9 +- Host Atoms: 7184 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.74 Hours +- Average Time Per Molecule: 0.53 Hours +- Total Nanoseconds Simulated: 1628.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/dg_plot.png b/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/dg_plot.png new file mode 100644 index 0000000..941f782 Binary files /dev/null and b/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/dg_results.csv b/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/dg_results.csv new file mode 100644 index 0000000..6396b21 --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/bace_ciordia_prospective/dg_results.csv @@ -0,0 +1,10 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +spiro16,49.60211134679863,0.07834431823238545,21.539887572309137,0.07490601278774633,-7.449728,-35.51195,0.10839161845389754,-8.18 +spiro5,48.944751374538285,0.07875724541970006,22.255466754933025,0.07374162424072037,-7.5123105,-34.20159,0.10789129182542243,-7.760000000000001 +spiro2,47.873229761351695,0.07588236603673194,24.375419830523853,0.0721011756795349,-7.6337633,-31.131573,0.10467431876875877,-7.03 +spiro10,57.407091343479706,0.08048217232273219,23.298709563225795,0.07429392434168772,-7.4880753,-41.59645,0.10953066810658271,-8.5 +spiro3,48.36970751878798,0.07866443060147059,18.26654245323657,0.07370217263329766,-7.618013,-37.721176,0.10779658108085799,-8.98 +spiro6,49.43660635249034,0.08109017766385687,21.50343990346194,0.07435043127983909,-7.5639467,-35.497116,0.1100163785308985,-9.53 +spiro4,45.52067086331629,0.08043111077792889,18.598316941117172,0.07447377338365352,-7.5339847,-34.456337,0.10961526582995294,-7.62 +spiro1,53.57085368075582,0.07841225204399604,25.046221636475547,0.0727281237121166,-7.5259066,-36.050537,0.10694793709696367,-7.52 +spiro15,54.237425413163905,0.08113144699916133,21.365700785028828,0.07568613927374782,-7.392897,-40.26462,0.11095360909111013,-9.05 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/README.md b/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/README.md new file mode 100644 index 0000000..99516f9 --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/README.md @@ -0,0 +1,33 @@ +# Bace P3 Arg368 In + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 27.44 +- RMSE: 27.65 +- R²: 0.13 +- Kendall 𝜏: 0.27 +- Spearman ρ: 0.41 + +## System Details +- Ligands: 21 +- Host Atoms: 6894 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 11.31 Hours +- Average Time Per Molecule: 0.54 Hours +- Total Nanoseconds Simulated: 3955.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/dg_plot.png b/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/dg_plot.png new file mode 100644 index 0000000..d5c151f Binary files /dev/null and b/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/dg_results.csv b/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/dg_results.csv new file mode 100644 index 0000000..1386bd9 --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/bace_p3_arg368_in/dg_results.csv @@ -0,0 +1,22 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +8a,44.62814520710166,0.08147652729763391,18.799447591792955,0.07406541794998024,-7.5808597,-33.40956,0.11010953926244238,-7.78985 +8b,45.6091175194077,0.08164565313985873,18.13976819542132,0.07390176216533509,-7.5205655,-34.989918,0.11012485245291308,-8.5129 +8c,53.94192858872584,0.07922086561491426,20.696323610869744,0.07474054567702124,-7.468239,-40.71384,0.10891324399206555,-8.30826 +8d,41.76394985767579,0.08028594823556826,20.089789026569317,0.0748481937581262,-7.5538116,-29.227974,0.10976377176891448,-8.34919 +8e,46.42895185984203,0.08263082061717263,17.92499148133508,0.07538763706650091,-7.4068165,-35.91077,0.11185324464823461,-8.4174 +8f,52.35678365127998,0.08354241958019613,21.007027529721846,0.07656883636995263,-7.40692,-38.756676,0.11332308931705895,-7.46243 +8g,56.393712209549506,0.08424192129790338,20.48433005221768,0.07825939384889251,-7.5136013,-43.422985,0.1149836250496488,-10.3546 +17a,48.704255032784175,0.08054906447404593,19.874515661310248,0.0735004185557685,-7.5017095,-36.331448,0.1090434010636002,-10.9413 +17b,43.636055167193895,0.0855750262370977,17.477384226266906,0.07490086571159606,-7.418782,-33.577454,0.11372433688453192,-11.5825 +17c,50.586312101520555,0.0820837655879458,21.253041732668617,0.07611375067543813,-7.453445,-36.786716,0.11194216191846393,-11.7462 +17d,48.51183156107531,0.0816900457214752,20.90765299224196,0.07691689279332263,-7.598482,-35.20266,0.11220281621668947,-11.3915 +17e,53.66122962665358,0.08448777439422787,19.807116359580053,0.07828845614969958,-7.3818827,-41.235996,0.1151836203129307,-11.9508 +17f,54.971326448140864,0.08554154385184008,21.18445134824548,0.07723235507067498,-7.423255,-41.21013,0.11524839432425553,-11.637 +17g,54.118015198079206,0.08566169224000074,19.832529008407363,0.07787871331363803,-7.414356,-41.69984,0.1157714105675854,-11.1186 +27a,41.68622516707761,0.08082758394948222,18.26186556328489,0.0757504262961706,-7.5934687,-31.017828,0.1107755632401035,-9.1541 +27b,44.96955200062334,0.08294924766288263,16.557899712464405,0.07655884334929823,-7.4247613,-35.83641,0.1128797332687344,-9.97264 +27c,52.597422545713535,0.08239154415446182,20.011807333372417,0.07625380395120601,-7.379099,-39.964714,0.11226312469010293,-10.0136 +27d,47.09107431005092,0.08461207143000253,18.533305598927033,0.07853486697441195,-7.5670047,-36.12477,0.11544231443610455,-9.27688 +27e,48.00599705340152,0.08662842835111316,17.58942665044937,0.07693846857184915,-7.3436975,-37.760265,0.11586204100034388,-9.35874 +27f,52.79899536900189,0.08468540448019318,19.704914218673363,0.07750665506158218,-7.3742666,-40.468346,0.11479938724056417,-9.09953 +27g,53.3344218799518,0.08751533874800653,19.561057795820716,0.08024164719568129,-7.435186,-41.20855,0.11873355238033823,-12.2509 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/README.md b/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/README.md new file mode 100644 index 0000000..6f6791f --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/README.md @@ -0,0 +1,33 @@ +# Ciordia Retro + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 29.55 +- RMSE: 29.60 +- R²: 0.34 +- Kendall 𝜏: 0.37 +- Spearman ρ: 0.51 + +## System Details +- Ligands: 32 +- Host Atoms: 7184 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 17.15 Hours +- Average Time Per Molecule: 0.54 Hours +- Total Nanoseconds Simulated: 5889.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/dg_plot.png b/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/dg_plot.png new file mode 100644 index 0000000..04abf8b Binary files /dev/null and b/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/dg_results.csv b/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/dg_results.csv new file mode 100644 index 0000000..fcdd4cb --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/ciordia_retro/dg_results.csv @@ -0,0 +1,33 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a,41.365622631950856,0.07530635812814886,15.540461200150428,0.07095001606903192,-7.348412,-33.173573,0.10346473966874367,-6.08468 +11,45.28847769947816,0.08024589103616232,14.061514948955361,0.07372291228423913,-7.4910135,-38.717976,0.108970045534804,-8.70337 +12,45.68488393900344,0.08079184543485392,13.838073601308032,0.07543392931748391,-7.523882,-39.370693,0.11053325282938381,-10.4569 +13,49.81042168241119,0.08228505077631361,18.482909466626158,0.0751784048610899,-7.5315094,-38.859024,0.1114568173721036,-9.64326 +14,44.17134185711036,0.08134819926903002,14.349832188353014,0.07723432663298321,-7.5007224,-37.32223,0.11217250436164897,-9.83624 +15,43.57198650903993,0.08021159321223664,13.091401877093372,0.07618760863462543,-7.49197,-37.972553,0.11062753452512704,-7.91744 +16,43.723721086551556,0.07961036924569614,14.74736782830441,0.0753021443826674,-7.5216236,-36.49798,0.10958204159470734,-7.05774 +17,46.76094084551305,0.08249702385515902,13.440991882567246,0.07590430735471806,-7.5199647,-40.839916,0.11210362536491933,-10.3651 +18,48.04578029462937,0.08164179412366405,13.80960905831709,0.0765005634794988,-7.5398073,-41.775978,0.11188261151944734,-9.90099 +19,47.71541731144749,0.08262228882734615,13.1935054260143,0.07545897004071409,-7.5417438,-42.063656,0.11189503461134813,-9.91084 +20,45.728192600468404,0.07980985694175569,13.462915474525358,0.07352952235309111,-7.619892,-39.885166,0.10851821931149272,-10.1676 +21,46.4191784383876,0.08159229640385,14.248603898675807,0.07522672568502972,-7.5141687,-39.68475,0.11097911105133444,-10.2153 +22,43.72309383791227,0.08412297376790404,12.584535938363766,0.07580871132661174,-7.5422196,-38.680775,0.11324149163869673,-7.60692 +23,45.281280523826595,0.08246646155257999,13.22383255885253,0.07855198299367634,-7.569442,-39.626892,0.11389087458283026,-9.81896 +24,41.949852662988114,0.08289558996610843,13.254325976786621,0.0744474906930262,-7.519945,-36.215473,0.11141861472086878,-9.78584 +25,43.39872177243747,0.08025230032094748,12.384555226781767,0.07635235014438987,-7.5011196,-38.515285,0.11077054247125027,-8.87004 +26,45.78475747809183,0.08107494270279578,16.162354228279973,0.07811741912332774,-7.533231,-37.155636,0.11258542314505582,-10.3651 +27,45.646642268937924,0.08082455428891966,13.512555426877778,0.07465645499251,-7.440225,-39.57431,0.11002815479708451,-9.61238 +28,42.61734876391925,0.08083099781823413,11.190103599261262,0.07446996725532001,-7.5723906,-38.999634,0.10990644308365094,-8.997 +29,44.74736370410669,0.0778968783323411,12.043048185208567,0.0737428679227104,-7.507441,-40.211758,0.10726571783841221,-8.73567 +30,41.86377146128126,0.08129272586014454,13.830326417684148,0.07479490205019715,-7.5374484,-35.570892,0.11046621497304594,-6.94738 +31,46.28676228070706,0.08165019567392366,17.236064327952704,0.07371361691873389,-7.534933,-36.585632,0.11000205349370472,-9.53354 +32,47.31793624705943,0.08178293047967625,16.861387761523638,0.07431921670105886,-7.532582,-37.98913,0.11050698479690099,-7.721520000000001 +33,49.38101490663168,0.07919499243423068,17.875765263481966,0.07408004877536079,-7.576414,-39.08167,0.10844215256632306,-7.13992 +34,46.50298210056918,0.07938509463682665,16.660806369015646,0.07404398028246835,-7.559585,-37.40176,0.10855645658627812,-10.2494 +35,47.938045269306116,0.08296745404106912,16.083102132263758,0.07424033699278379,-7.5060453,-39.36099,0.11133384960046525,-9.88176 +36,52.54125950125601,0.0837713063576074,16.3654341046972,0.07850532905313662,-7.520141,-43.695965,0.11480731012701835,-10.9787 +37,49.508686693179094,0.0804292617148868,16.927234873323236,0.07483589609345993,-7.532482,-40.113934,0.10986026344458169,-9.45002 +38,48.075737946937664,0.08062748806327792,16.373923288140986,0.07628452425353537,-7.571693,-39.273506,0.11099603809137625,-9.38493 +39,48.38072803863606,0.07939791067237056,19.149848633478953,0.07540409351213315,-7.5246787,-36.75556,0.10949797047217019,-9.36077 +40,47.94953013017207,0.07897667791466688,18.390083743316335,0.07238443105901243,-7.504692,-37.064137,0.10712992819083729,-8.64597 +41,50.68263037388527,0.08142852980621108,18.18985748273236,0.07511494161519,-7.5648575,-40.057632,0.11078294056511775,-9.10997 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/README.md b/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/README.md new file mode 100644 index 0000000..c7ed96f --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/README.md @@ -0,0 +1,33 @@ +# Keranen P2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 27.77 +- RMSE: 27.95 +- R²: 0.00 +- Kendall 𝜏: -0.14 +- Spearman ρ: -0.15 + +## System Details +- Ligands: 12 +- Host Atoms: 6252 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.64 Hours +- Average Time Per Molecule: 0.55 Hours +- Total Nanoseconds Simulated: 2313.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/dg_plot.png b/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/dg_plot.png new file mode 100644 index 0000000..ffea745 Binary files /dev/null and b/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/dg_results.csv b/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/dg_results.csv new file mode 100644 index 0000000..0fe94a9 --- /dev/null +++ b/summaries/2026_jun_08_abfe/janssen_bace/keranen_p2/dg_results.csv @@ -0,0 +1,13 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +29,49.612687247213216,0.08311390023184502,16.537035593095844,0.07948585504435982,-7.489121,-40.564777,0.11500400672968776,-9.99 +30,43.97275572120828,0.08327874722449619,15.465614983820394,0.07920664515292253,-7.45936,-35.9665,0.11493059808276697,-10.36 +31,45.83214627433902,0.085547021719357,14.096624603928186,0.07892211109721976,-7.477599,-39.21312,0.1163915484263958,-10.36 +32,47.70504637191729,0.08340116064001404,13.38849784717113,0.07871168552476084,-7.94728,-42.26383,0.11467904357052457,-10.36 +33,44.04809755348727,0.08751970835871326,13.934882624690456,0.0794987191111542,-7.441512,-37.554726,0.1182359746080203,-10.24 +34,51.161002996789826,0.08507360708719927,13.393937913861665,0.07850805440498332,-7.2562094,-45.023273,0.11576283181264609,-10.15 +35,40.03975619108547,0.08505531385958733,11.683897107603878,0.07902995925015188,-7.4431252,-35.79898,0.11610400886633318,-9.81 +36 out,45.92457087519259,0.08193872801036843,16.132035667591634,0.07510697847920417,-7.5353994,-37.327934,0.11115310775787052,-10.36 +37 out,41.659311805807754,0.08358005833494243,15.820804100586308,0.07642930229097465,-7.6554556,-33.493965,0.11325663071077809,-10.56 +39 out,46.710401459883485,0.08305997194615325,19.357865281012657,0.07649041765824707,-7.4397945,-34.792328,0.11291475958982881,-9.68 +38 out,45.26707346693803,0.08616896456749573,15.702039192734171,0.07579522347030755,-7.5494843,-37.114517,0.11476064811401249,-10.49 +28 out,43.97545116203282,0.08138686834807127,14.445254246909668,0.07623047205841713,-7.496969,-37.027164,0.1115119151021782,-10.49 diff --git a/summaries/2026_jun_08_abfe/mcs_docking_set/hne/README.md b/summaries/2026_jun_08_abfe/mcs_docking_set/hne/README.md new file mode 100644 index 0000000..a9d1065 --- /dev/null +++ b/summaries/2026_jun_08_abfe/mcs_docking_set/hne/README.md @@ -0,0 +1,33 @@ +# Hne + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 17.39 +- RMSE: 17.70 +- R²: 0.28 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.47 + +## System Details +- Ligands: 17 +- Host Atoms: 3804 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 7.09 Hours +- Average Time Per Molecule: 0.42 Hours +- Total Nanoseconds Simulated: 3185.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/mcs_docking_set/hne/dg_plot.png b/summaries/2026_jun_08_abfe/mcs_docking_set/hne/dg_plot.png new file mode 100644 index 0000000..bc303ca Binary files /dev/null and b/summaries/2026_jun_08_abfe/mcs_docking_set/hne/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/mcs_docking_set/hne/dg_results.csv b/summaries/2026_jun_08_abfe/mcs_docking_set/hne/dg_results.csv new file mode 100644 index 0000000..3841014 --- /dev/null +++ b/summaries/2026_jun_08_abfe/mcs_docking_set/hne/dg_results.csv @@ -0,0 +1,18 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +6,23.76890949376904,0.0844465189999311,4.426603268406102,0.07712074870756112,-7.574325,-26.916632,0.1143626882003939,-7.03256 +14,25.14305045687249,0.07878266405009966,5.888934406126795,0.07556257048317486,-7.7969885,-27.051105,0.10916231132060017,-10.3255 +15,27.56826458305803,0.08583357455207734,10.656897263848698,0.0797608952798776,-7.788741,-24.70011,0.11717168146030262,-12.2782 +16,82.28307207410471,0.08981906252387208,60.91031120157762,0.08230903715858663,-7.8025866,-29.175348,0.1218287387714444,-11.8386 +17,30.39735184192847,0.08222992635778653,10.312059466128543,0.07585357932378074,-7.923873,-28.009163,0.11187281298437118,-11.414 +18,24.61334931667846,0.07963215711991428,7.401242192761281,0.07443943076625033,-7.7817984,-24.993904,0.10900692317634735,-10.7585 +19,86.96325928104508,0.08798858730037513,64.34090046180542,0.08067621965318324,-7.785045,-30.407404,0.11937606088594314,-11.536 +20,28.711236279076612,0.07854242849322864,10.118128408412195,0.07332086498281992,-7.9151797,-26.508291,0.10744702097053618,-10.5033 +21,29.81509737550743,0.08556666727012781,13.987983010695967,0.08153464001217642,-7.765845,-23.592958,0.11819285963894757,-12.2782 +22,25.485022625946197,0.07753693653799609,6.498085346329223,0.07247375342362053,-7.8934,-26.880337,0.10613397883338295,-11.3613 +23,32.149607987757705,0.08140453378167507,10.43010340430862,0.07582717155215037,-7.8608036,-29.580307,0.11124953063186882,-10.3711 +25,22.509993247188948,0.0780143770115824,3.7479358032310337,0.07323840495371109,-7.973309,-26.735365,0.10700517268183389,-11.9998 +26,26.379289775222944,0.0791402985047546,4.82167250210919,0.07349056054268627,-7.9347405,-29.492357,0.10800022840855429,-12.5809 +27,30.529638169138035,0.07846428828158143,2.587538184319486,0.07546098410749526,-7.780417,-35.72252,0.10886231973463899,-14.488 +28,43.620077669069964,0.08249494986439786,14.036924008668723,0.07740844912254188,-7.959068,-37.54222,0.11312596849833671,-12.6433 +29,36.84613445547501,0.08395540062758534,10.766309818962407,0.07812883710634297,-7.8217087,-33.901535,0.11468489212676547,-13.8977 +30,44.086256494594004,0.0848152714655595,18.92022520847786,0.07927814992525835,-7.744752,-32.910778,0.11609761121292846,-13.0996 diff --git a/summaries/2026_jun_08_abfe/mcs_docking_set/renin/README.md b/summaries/2026_jun_08_abfe/mcs_docking_set/renin/README.md new file mode 100644 index 0000000..a169f44 --- /dev/null +++ b/summaries/2026_jun_08_abfe/mcs_docking_set/renin/README.md @@ -0,0 +1,33 @@ +# Renin + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 37.75 +- RMSE: 38.13 +- R²: 0.01 +- Kendall 𝜏: -0.08 +- Spearman ρ: -0.11 + +## System Details +- Ligands: 29 +- Host Atoms: 5321 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 15.19 Hours +- Average Time Per Molecule: 0.52 Hours +- Total Nanoseconds Simulated: 5578.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/mcs_docking_set/renin/dg_plot.png b/summaries/2026_jun_08_abfe/mcs_docking_set/renin/dg_plot.png new file mode 100644 index 0000000..1d4f933 Binary files /dev/null and b/summaries/2026_jun_08_abfe/mcs_docking_set/renin/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/mcs_docking_set/renin/dg_results.csv b/summaries/2026_jun_08_abfe/mcs_docking_set/renin/dg_results.csv new file mode 100644 index 0000000..f464a16 --- /dev/null +++ b/summaries/2026_jun_08_abfe/mcs_docking_set/renin/dg_results.csv @@ -0,0 +1,30 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +b1i5k_xray,54.22025454912219,0.08649878592360173,23.373005756989023,0.08098254959786055,-7.6945295,-38.541775,0.11849140604122742,-11.8676 +b1i5j,67.1989764046547,0.08574652776854402,25.318003587032937,0.0797203028670252,-7.621096,-49.502068,0.11708028746792484,-11.4568 +b1i2n,50.164947903828555,0.08324480407245678,21.146044416139514,0.07957084859065863,-7.629885,-36.648785,0.11515735908095165,-10.9765 +b1i5i,75.16859642100279,0.0842271695936919,27.053943376432382,0.07956979619606094,-7.7853703,-55.90003,0.11586875577327657,-11.4568 +b1i5h,55.34885022651635,0.08385541215103556,22.023505272962957,0.07935545569088442,-7.4658146,-40.79116,0.1154513685277397,-10.8059 +b1i5l,65.1893470537444,0.08815790041112491,21.906019085329852,0.07767130407446267,-7.3494706,-50.632797,0.1174931780212173,-9.653 +b1i5n,70.96730335742828,0.09297904125380262,25.359885950590197,0.08180267172845099,-7.7313886,-53.338802,0.12384175069171562,-10.2436 +b1a2m,63.95666715059149,0.08175810376903427,23.007969218327716,0.0791346519962964,-7.368987,-48.317684,0.1137834815712857,-9.60566 +b1i2o,65.17825491558098,0.08200449962193632,23.88900970645703,0.0787963393277558,-7.6942225,-48.983467,0.11372599109130238,-10.5657 +b1i5o,66.12216349633094,0.0860910327494362,31.321803597476997,0.08347706721416169,-7.4546494,-42.255005,0.119916999089129,-10.0361 +b1i4i,62.993867780371836,0.08433835822449391,24.191174628728458,0.07910538976603429,-7.809032,-46.61172,0.11563140299260952,-8.7908 +b1i4e,62.14067004585741,0.08939816643348417,22.10338001718498,0.07894345388397622,-7.546259,-47.583546,0.11926483586036757,-10.1889 +b1i4g,61.109966909581814,0.08548032767992424,25.209283404529717,0.08025783659816113,-7.3660107,-43.26669,0.11725274732680832,-8.35437 +b1i1,65.0466572724105,0.08153166857100963,22.85288043916678,0.07786605996762429,-7.8841786,-50.077953,0.11274101416456488,-7.39449 +b1i2a,65.6850541013396,0.08146232213174785,23.568898495394535,0.07892341764237608,-7.6881566,-49.80431,0.1134240529140516,-8.69953 +b1i2e,63.15161322307961,0.08455907230358375,22.931567394408283,0.07873250497626977,-7.551793,-47.77184,0.11553806320291617,-10.4744 +b1i2i,64.79903219232125,0.08339987006165393,24.52133975286398,0.08004317078135084,-7.560901,-47.838593,0.11559605319833915,-9.81412 +b1i2j,59.00021518826446,0.08419399723628913,22.647238828761523,0.08006868571913847,-7.373313,-43.72629,0.11618788062192387,-11.3246 +b1i5c,72.8565496935868,0.08370375798215883,27.7297301893699,0.07938668716131354,-7.737054,-52.863873,0.1153627548162061,-11.8676 +b1i5b,64.29778734277882,0.08547905411194306,21.608342990147815,0.07957121071777666,-7.6830664,-50.372517,0.11678290228867112,-8.00772 +b1i2k,61.04060993918916,0.0838874361144049,21.13292689163689,0.07745487173600796,-7.5236287,-47.431313,0.11417687635195582,-10.6355 +b1i2h,67.39337579520851,0.08317258120484701,22.039819153848075,0.0775391397634975,-7.4754214,-52.828976,0.11371014228968349,-9.82353 +b1i2g,67.23048422671222,0.08442835240939979,20.940229939461613,0.0776879041367982,-7.6944532,-53.984715,0.11473254612242399,-8.338 +b1i4b,65.41955217680976,0.08535087272045658,21.80541370106577,0.07786137875586004,-7.57529,-51.189423,0.11552993454471906,-8.39094 +b1i5a,67.42613832770164,0.08666910904424348,22.25654860625934,0.07844198793454991,-7.445604,-52.615192,0.11689602188974199,-10.3953 +b1i2d,62.15535242192124,0.08698417141053666,17.441527198183987,0.07921995148510556,-7.4052243,-52.11905,0.11765222815263679,-8.41399 +b1i4a,60.929911345618514,0.0852940292352867,24.94318919917,0.0793344624735117,-7.674982,-43.661705,0.11648617239462794,-7.23542 +b1i5d,59.88068527006177,0.08818592164087428,29.293473100298744,0.08178326373285882,-7.721149,-38.30836,0.12027160513790759,-11.2166 +b1i2c,54.18148026854657,0.0840694430363736,20.91092741948565,0.07937024262149583,-7.2929635,-40.56352,0.11561706909553268,-6.88372 diff --git a/summaries/2026_jun_08_abfe/merck/cdk8/dg_results.csv b/summaries/2026_jun_08_abfe/merck/cdk8/dg_results.csv new file mode 100644 index 0000000..e57b783 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/cdk8/dg_results.csv @@ -0,0 +1,2 @@ +mol,solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol) +43,9.34169046859635,0.07621601985100207 diff --git a/summaries/2026_jun_08_abfe/merck/cmet/README.md b/summaries/2026_jun_08_abfe/merck/cmet/README.md new file mode 100644 index 0000000..e972a5c --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/cmet/README.md @@ -0,0 +1,33 @@ +# Cmet + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 33.73 +- RMSE: 34.18 +- R²: 0.57 +- Kendall 𝜏: 0.62 +- Spearman ρ: 0.74 + +## System Details +- Ligands: 24 +- Host Atoms: 4977 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 11.26 Hours +- Average Time Per Molecule: 0.47 Hours +- Total Nanoseconds Simulated: 4420.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/cmet/dg_plot.png b/summaries/2026_jun_08_abfe/merck/cmet/dg_plot.png new file mode 100644 index 0000000..c98ff3e Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/cmet/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/cmet/dg_results.csv b/summaries/2026_jun_08_abfe/merck/cmet/dg_results.csv new file mode 100644 index 0000000..9416fcb --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/cmet/dg_results.csv @@ -0,0 +1,25 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3402753_200,33.424539339220345,0.07671635139924092,1.9489106433082979,0.07397579239053068,-6.894729,-38.370358,0.10657305678180912,-9.13905 +CHEMBL3402747_3400,30.13888152829939,0.07518827276150691,3.1294907949248754,0.06997731392912003,-6.894312,-33.9037,0.10271368373100724,-7.46041 +CHEMBL3402744_300,36.67583299662962,0.0765799295411143,6.8087234045035965,0.07245492212986428,-6.9629393,-36.830048,0.10542391260699219,-8.89882 +CHEMBL3402745_200,38.19589596045311,0.07547275640937988,6.071954029602892,0.07379366688777823,-6.8967247,-39.020664,0.10555397781596848,-9.13905 +CHEMBL3402750_400,33.517559918178314,0.07415389848402194,1.313750135417033,0.07259869789306901,-6.8803377,-39.08415,0.10377558285139976,-8.72837 +CHEMBL3402743_42,58.44328271543549,0.08374958869157946,20.253178838868745,0.08075804931282551,-7.1847,-45.374798,0.11634369830300863,-10.0637 +CHEMBL3402752_30000,27.587619744010535,0.07527692592089998,1.5682385837980892,0.07352327726386383,-6.876743,-32.896122,0.1052249394189403,-6.17032 +CHEMBL3402755_4200,35.76379363826056,0.07673437278716533,3.5651984842664013,0.07230322730482638,-6.879207,-39.0778,0.10543206649655051,-7.33522 +CHEMBL3402749_500,32.96989203190459,0.07464249661440096,2.8001451881001307,0.07370297436204522,-6.8759613,-37.04571,0.10489819221818436,-8.59616 +CHEMBL3402765_11-charged-pKa-8.1,63.643777148473326,0.083327550791352,19.289372510369606,0.07991943823676793,-6.8953757,-51.24978,0.11545820598366281,-10.8575 +CHEMBL3402742_23,59.48571899602261,0.08453403200546514,18.97028622658319,0.07990696891771867,-7.147846,-47.663277,0.11632336931467495,-10.4205 +CHEMBL3402754_40,34.86631999640436,0.07468974729351621,2.2576832320233846,0.07414631495731187,-6.8830795,-39.49171,0.10524369041666204,-10.0926 +CHEMBL3402748_5300,32.364034475818144,0.07565129667987726,6.322611885343693,0.07366637661727259,-6.8962984,-32.937717,0.10559286781437775,-7.19739 +CHEMBL3402741_400,64.6084486542451,0.08554097449851204,15.205456657120553,0.08228889707741625,-6.8229394,-56.225933,0.11869591779152598,-8.72837 +CHEMBL3402763_90,58.24409203082448,0.08471725297835257,13.613165735234105,0.08078607146477111,-7.1133437,-51.744267,0.11706153208851017,-9.61215 +CHEMBL3402764_90,59.50625370826385,0.0839894122435669,21.743078220885952,0.07755252832324913,-6.8555627,-44.618736,0.11431804764930245,-9.61215 +CHEMBL3402751_2100,30.128758506488623,0.0750155209441822,1.2501843968553386,0.07236352801775311,-6.86866,-35.747234,0.10422959545975019,-7.745890000000001 +CHEMBL3402756_2.7 redocked,61.451233111391986,0.08384290758253783,21.137178848724467,0.07979236126452689,-7.0471168,-47.36117,0.11574305192132595,-11.6897 +CHEMBL3402762_1 redocked,62.95372454330743,0.08999304981475777,21.96556856451318,0.08136035268758117,-7.074184,-48.06234,0.12131881966294046,-12.2782 +CHEMBL3402760_1 redocked,66.65427658650741,0.08611275956676576,22.5078179962629,0.08061756411430707,-7.2458224,-51.392284,0.11796015854485793,-12.2782 +CHEMBL3402757_6.5 redocked,62.223618332917795,0.09142121209004488,22.78243379455821,0.0828509402179716,-7.0467114,-46.487896,0.12337794095791546,-11.1692 +CHEMBL3402761_1 redocked,51.5752182445652,0.08180643373279178,7.768587254092384,0.0801614860663501,-7.3366313,-51.143265,0.114534520771876,-12.2782 +CHEMBL3402758_10 redocked,62.35169130326144,0.08284974383873171,23.016057115029746,0.08040940080877118,-7.363319,-46.698956,0.1154545442698947,-10.914 +CHEMBL3402759_5.7 redocked,63.24733455818346,0.08619360605956354,21.45674987855507,0.0813583615937764,-6.987903,-48.778492,0.11852645580955713,-11.247 diff --git a/summaries/2026_jun_08_abfe/merck/eg5/README.md b/summaries/2026_jun_08_abfe/merck/eg5/README.md new file mode 100644 index 0000000..a00c317 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/eg5/README.md @@ -0,0 +1,33 @@ +# Eg5 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 24.11 +- RMSE: 24.39 +- R²: 0.42 +- Kendall 𝜏: 0.46 +- Spearman ρ: 0.60 + +## System Details +- Ligands: 28 +- Host Atoms: 5906 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 13.96 Hours +- Average Time Per Molecule: 0.50 Hours +- Total Nanoseconds Simulated: 5138.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/eg5/dg_plot.png b/summaries/2026_jun_08_abfe/merck/eg5/dg_plot.png new file mode 100644 index 0000000..d5f3d13 Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/eg5/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/eg5/dg_results.csv b/summaries/2026_jun_08_abfe/merck/eg5/dg_results.csv new file mode 100644 index 0000000..212edef --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/eg5/dg_results.csv @@ -0,0 +1,29 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1078774,27.34432436542634,0.07878536584890523,2.0394135618889933,0.07206554628412622,-7.092659,-32.397568,0.10677348375498188,-10.6625 +CHEMBL1093087,49.39147600997283,0.0850334909903914,12.878850136339937,0.08109475686587254,-6.998875,-43.5115,0.11750342199760805,-10.5962 +CHEMBL1082249,43.38306752934819,0.08119495940283056,13.590624008821521,0.0776122297539039,-6.9802475,-36.77269,0.11232221347445068,-11.2832 +CHEMBL1089393,22.598452452426354,0.0715884668400687,0.8305152397607514,0.06804035084064027,-7.0447416,-28.812677,0.09876435554909996,-8.42983 +CHEMBL1078691,29.9454216643838,0.07733974009114808,4.55930916881523,0.07199319105065359,-7.145865,-32.53198,0.10566198443632528,-10.2494 +CHEMBL1086409,47.50697080557586,0.07976973422834968,18.33034392396072,0.07493576887592442,-7.122125,-36.298748,0.10944669915482835,-9.93104 +CHEMBL1082248,42.02374101552296,0.0792852411156195,17.30591269314748,0.07522202796901904,-7.0148106,-31.732643,0.10929090973422174,-11.6963 +CHEMBL1084678,57.27089557195657,0.0882889108621891,25.277737216895957,0.08210669818616961,-7.119253,-39.11241,0.12056716662618527,-11.1913 +CHEMBL1084115,23.745905356934312,0.07903988744739258,-1.157429394831912,0.06946928393855117,-7.28324,-32.186573,0.10522967841170823,-9.49772 +CHEMBL1084431,38.93495570738296,0.08669516909349677,13.254556241648753,0.08184391884511633,-6.9873714,-32.667774,0.11922449159495704,-9.86313 +CHEMBL1085895,32.26738029915933,0.08380804356108738,9.170194624348659,0.07955387418163926,-7.025738,-30.122923,0.11555348139647377,-10.9219 +CHEMBL1084677,64.11918005579106,0.08789404060837694,29.296491182190614,0.08053990113593815,-6.9619083,-41.7846,0.11921425271104838,-11.5248 +CHEMBL1077227,45.915183422621986,0.0956507527473042,15.490044942814393,0.07842454052365115,-7.0711207,-37.49626,0.12369104679592505,-11.3918 +CHEMBL1086410,40.8687673773231,0.0815632248448281,15.225432401733178,0.07494673150332828,-7.075698,-32.71903,0.11076810104953484,-11.5248 +CHEMBL1083517,56.11408727085572,0.08180101372106774,23.9992379868545,0.07568868702002345,-7.065135,-39.17998,0.1114458756016093,-11.5248 +CHEMBL1096003,58.763334661086525,0.08784470910377819,24.469195668200094,0.0800247729532686,-6.917909,-41.212048,0.11883037155436989,-11.938 +CHEMBL1077204,42.01481820530355,0.08837979654634082,13.576057939858998,0.0786082805601949,-6.9504833,-35.38924,0.11828038810471882,-11.1117 +CHEMBL1083836,43.13304965115713,0.08160993471506801,16.557495597415727,0.07706756874175989,-7.0576735,-33.63323,0.11224790241231036,-10.9219 +CHEMBL1085666,54.015057409254425,0.0840671326772264,25.517556767484198,0.0744355366069031,-7.122624,-35.62012,0.11228504756434847,-10.5656 +CHEMBL1085692,39.28876428549147,0.09026039960733893,8.63354618930346,0.07789716320470154,-6.9417744,-37.596992,0.11922628809376067,-11.3918 +CHEMBL1084143,50.306920458635425,0.0862135321649445,16.615480141114496,0.08306310783197775,-7.194256,-40.8857,0.11971738808987892,-11.938 +CHEMBL1096002,42.22120425431483,0.07996058648303987,14.718012402482756,0.07642886194684385,-6.987406,-34.490597,0.11061223408466812,-11.1913 +CHEMBL1089056,19.29697520866227,0.07760340181031496,-0.834464978085872,0.0699201967164931,-7.0315843,-27.163025,0.10445631566069276,-9.49772 +CHEMBL1093088,29.397087824203155,0.07720400976871522,3.1404980465425147,0.07224767609300603,-7.129299,-33.385887,0.10573639782595107,-11.2832 +CHEMBL1084676,43.62466126772498,0.08803266923757226,14.222113406249054,0.07972777387907638,-7.023826,-36.426373,0.11876981426610439,-10.7782 +CHEMBL1084935,32.546245779197314,0.08313462609269971,5.030748459423033,0.0797787752237751,-6.984483,-34.499985,0.11522160835441685,-10.5962 +CHEMBL1078998,22.191719204978607,0.0780448831125867,-1.3023347666356548,0.06879808333781441,-7.1556935,-30.649746,0.10403931973544511,-10.4326 +CHEMBL1088740,21.243794727692194,0.07245798377569274,0.8831084225175196,0.06853046254087884,-7.0853744,-27.446062,0.09973256092623586,-8.75107 diff --git a/summaries/2026_jun_08_abfe/merck/hif2a/README.md b/summaries/2026_jun_08_abfe/merck/hif2a/README.md new file mode 100644 index 0000000..14bff99 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/hif2a/README.md @@ -0,0 +1,33 @@ +# Hif2A + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 24.66 +- RMSE: 24.85 +- R²: 0.12 +- Kendall 𝜏: 0.21 +- Spearman ρ: 0.31 + +## System Details +- Ligands: 41 +- Host Atoms: 1770 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 13.05 Hours +- Average Time Per Molecule: 0.32 Hours +- Total Nanoseconds Simulated: 6642.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/hif2a/dg_plot.png b/summaries/2026_jun_08_abfe/merck/hif2a/dg_plot.png new file mode 100644 index 0000000..c5faf2d Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/hif2a/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/hif2a/dg_results.csv b/summaries/2026_jun_08_abfe/merck/hif2a/dg_results.csv new file mode 100644 index 0000000..a155b6e --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/hif2a/dg_results.csv @@ -0,0 +1,42 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1,34.24895859894946,0.07281723977680216,4.942198756576502,0.07141484872605192,-7.821437,-37.128193,0.10199230866725774,-11.3247 +7a,30.976618209266558,0.07364131813601245,4.134809084545551,0.07093720778687225,-7.8651233,-34.706932,0.10225033586941065,-9.99707 +7b,25.695710463883294,0.07395502375876575,1.7795040934584534,0.07121478633027058,-7.69236,-31.608562,0.10266884304026075,-7.39451 +15,35.13527248956537,0.07257917578405189,8.14600156787548,0.07240204715302427,-7.826878,-34.816147,0.10251728239395079,-11.0462 +23,32.40918244087338,0.07273699516807157,6.1370804258155145,0.07308379766091133,-7.718385,-33.990482,0.10311116305532149,-7.06742 +25,37.51166023696938,0.07172381548171648,8.168215192589976,0.07183572922702455,-7.9081035,-37.251553,0.10151195841295597,-10.2831 +30,32.73832884234216,0.07093547972750851,4.667198464119029,0.06912340870595288,-7.618729,-35.68986,0.09904487828909667,-10.5657 +31,33.30928337385934,0.07055156611388932,5.8971853834589,0.0715124919935375,-8.022928,-35.435024,0.10045675682724513,-8.84235 +41,32.54665155239217,0.07215245195557507,4.140893227260099,0.07142651704037684,-7.8058934,-36.21165,0.10152696026041956,-9.78701 +42,33.16713180171325,0.07330940561886061,6.9529679798458215,0.07027185141123686,-7.842466,-34.056633,0.10154999779888517,-8.93969 +43,37.27820348071426,0.07006083624952483,8.093127126074494,0.0695298930446091,-7.6396575,-36.82473,0.0987062652660788,-8.69946 +50,27.82470420262534,0.07285259822709034,5.814694679798542,0.06857063538887262,-7.6530466,-29.663055,0.10004715441266462,-9.69694 +54,33.74491070622632,0.0745760844309448,6.809904924581861,0.07229133251553807,-7.5418763,-34.47688,0.1038635120045702,-9.3095 +57,32.42006314855723,0.07307044356967446,3.21731971838086,0.07133295922492044,-7.626177,-36.82892,0.10211601635029219,-10.6737 +61,31.311912437465093,0.06992168581145176,6.932045455374881,0.07092940557873972,-7.912317,-32.292187,0.09959931085338256,-10.1076 +67,31.293222341965517,0.06969505579505196,0.7035979559097867,0.06641866133828515,-7.671803,-38.26143,0.09627481174349405,-10.1717 +84,26.157932689257773,0.07371831732869108,5.429786581629866,0.07004373299017398,-7.75162,-28.479763,0.10168832204817023,-7.57545 +124,26.964001473679144,0.0710162001585041,-2.1066905843764205,0.06847676926242119,-7.8127728,-36.883465,0.09865276789614971,-10.123 +155,35.350544616354334,0.07441701572165137,7.947203042591158,0.0717684365476117,-7.9505367,-35.353878,0.10338568911317018,-10.5033 +156,38.04650459803258,0.07416825867900435,9.05819921401283,0.07091295844520153,-7.677491,-36.665794,0.10261373334464828,-9.73619 +163,33.682434877126546,0.07397300642184176,10.064912839422549,0.07105373096945956,-7.756807,-31.37433,0.10257016312635064,-11.0103 +164,31.95089898639278,0.07449709257987244,9.284626614749584,0.07154528573719855,-7.6824803,-30.348751,0.10328864755659971,-6.76476 +165,30.49306669557363,0.07759564030417622,8.807594228543348,0.07070687546393989,-7.636381,-29.321856,0.1049787865813289,-9.23534 +167,37.75219288691896,0.07134489084164482,9.680153209843297,0.07268519351791423,-7.961822,-36.033855,0.10184905893498897,-10.6737 +206,34.781086510465556,0.07101575937826458,9.138201506953479,0.07177984613405114,-7.62794,-33.270824,0.10097318649572089,-10.123 +215,35.073500927834786,0.07263130567527572,9.314320667730021,0.0737744982553785,-7.669061,-33.42824,0.10352769270551809,-10.5996 +224,40.74903492036664,0.06938096311388506,7.803782998292476,0.07119316529394018,-7.887872,-40.833122,0.09940917878737641,-9.66013 +227,34.508599110526816,0.07120167150139826,5.46668919221498,0.07097922328676032,-7.7289524,-36.77086,0.10053719790696779,-10.7585 +231,35.70288834091643,0.07424700737030318,10.654184382943798,0.07242314566131698,-7.689045,-32.73775,0.10371947806909844,-10.0228 +234,37.868716641843214,0.07458298034582804,10.038968698713603,0.07182538679393845,-7.6586075,-35.488354,0.1035447108517139,-10.3478 +235,38.169475396747536,0.07356614570775952,8.87876667371637,0.071859139703711,-7.6530104,-36.94372,0.10283828933453122,-10.123 +237,26.08353790780213,0.07328457493786895,6.3730764045378185,0.07278637949292399,-7.7434764,-27.45394,0.10328836315632113,-9.54973 +251,36.26548217151287,0.07171468776635181,10.671175054958317,0.07247897151568396,-7.683953,-33.27826,0.10196174651994078,-10.2436 +252,44.036092380136154,0.07169413774227798,17.130205306792366,0.07345822221879544,-7.685645,-34.591534,0.1026457977617918,-9.71233 +254,41.34483973950654,0.07293285372794116,13.442278753745411,0.07403100495392899,-7.827145,-35.72971,0.10392204216329622,-9.54973 +256,38.0430973194896,0.07164522349881765,14.09781629358694,0.07229914113879693,-7.7430415,-31.688322,0.10178508662669207,-10.6737 +266,38.104859092693765,0.07183227576447393,8.546248732468577,0.07257340145567324,-7.7162437,-37.274853,0.1021115783853611,-10.5337 +289,35.58966385038926,0.07072622374018299,10.751647688713987,0.07259102116339355,-7.760092,-32.598106,0.10134917403753559,-10.914 +290,39.98143847195081,0.07229196470345903,3.3080293750714778,0.07038038615964319,-7.643355,-44.316765,0.10089364160672692,-10.5657 +336,37.30889530963156,0.07370041229305409,15.79264786013673,0.07250812487477802,-7.6211705,-29.137419,0.1033884855533853,-9.82348 +338,44.46949723567141,0.07372942584651862,16.960579575254,0.07320297636059081,-7.64193,-35.150845,0.10389756485936764,-10.7585 diff --git a/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/README.md b/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/README.md new file mode 100644 index 0000000..82a71ac --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/README.md @@ -0,0 +1,33 @@ +# Hif2A Jmc2023 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 25.47 +- RMSE: 25.74 +- R²: 0.10 +- Kendall 𝜏: 0.22 +- Spearman ρ: 0.28 + +## System Details +- Ligands: 38 +- Host Atoms: 1937 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 10.97 Hours +- Average Time Per Molecule: 0.29 Hours +- Total Nanoseconds Simulated: 5597.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/dg_plot.png b/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/dg_plot.png new file mode 100644 index 0000000..ba903b3 Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/dg_results.csv b/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/dg_results.csv new file mode 100644 index 0000000..34c7ad4 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/hif2a_jmc2023/dg_results.csv @@ -0,0 +1,39 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +22a,,,8.57948885345495,0.07101768049028588,,,,-8.347403690247063 +22b-bindingpose2,31.24130171816379,0.07061518240768863,8.565666984428411,0.06980761769131957,-8.002366,-30.678003,0.09929555616546276,-8.347403690247063 +22b-bindingpose1,30.414420502065873,0.07409084228415377,8.440984514367862,0.07121263665710041,-7.8199615,-29.793398,0.1027652301609428,-8.347403690247063 +22e-bindingpose1,,,10.731247139588366,0.07056437142868201,,,,-8.845393034318414 +22e-bindingpose2,36.64215874580561,0.07109624639876351,10.876727663466587,0.07176831290363515,-8.035061,-33.800495,0.10102161644434214,-8.845393034318414 +22d-bindingpose2,,,11.764603264993065,0.07085090975965333,,,,-8.35463001826214 +22d-bindingpose1,28.57209735395786,0.07164995193693714,11.735873237757373,0.0702560404284607,-7.919616,-24.755842,0.100347530259847,-8.35463001826214 +22g-bindingpose1,35.26484004016677,0.07229659324804137,7.89035690104641,0.07040235743984193,-7.7871537,-35.16164,0.10091228531928115,-9.64592859056722 +22f-bindingpose1,35.54192434966379,0.06916300054734731,10.839249509732332,0.07217755412510608,-7.8932533,-32.59593,0.09996559390207704,-9.166723754816239 +22g-bindingpose2,33.299765367836066,0.07521994834794625,7.894136500235129,0.07074519135904205,-7.825278,-33.230907,0.10326142905216439,-9.64592859056722 +22f-bindingpose2,,,11.105485035764602,0.07193472944040748,,,,-9.166723754816239 +35e,35.056930860294045,0.06837411503893649,7.375973050273649,0.06980501850818445,-7.6311846,-35.31214,0.09771264102604993,-9.800757479938321 +35f,29.631203889916936,0.07217290905936484,7.747064035845832,0.06994063115767606,-7.682781,-29.566923,0.10050184420609123,-8.954086721804785 +35i,34.12750108606477,0.07142170171209124,6.321086600509436,0.07157726378533774,-7.8407154,-35.64713,0.10111559803732931,-9.780546569457208 +35g,35.34204356255179,0.07087245866338697,7.658798306412563,0.07054995101671721,-7.8494544,-35.5327,0.10000100492222412,-9.67851401006101 +35c,30.372031593292487,0.06954307526080068,8.476199647766283,0.06947591393001679,-7.6731668,-29.569002,0.09830128144200607,-8.829058731396596 +35d,40.7411089092273,0.06575178533744393,8.061717623521844,0.06870630239371979,-7.8713527,-40.550743,0.0950991759358543,-8.91561112972059 +35j-S,41.2967112099429,0.06868605743360008,5.997914994667278,0.07187181147844367,-7.7858143,-43.084614,0.09941494742223,-10.022270579071401 +35j-R,34.0935897792476,0.06951861050939778,6.3496675023134985,0.0720380948067987,-7.90382,-35.64774,0.100111559325338,-10.022270579071401 +35h-S,34.789990992556,0.07203994428744576,6.368292732608723,0.07129729744003893,-7.7723236,-36.19402,0.10135609599423051,-8.91561112972059 +35s,33.06854237965613,0.06963953250937116,7.973727096657289,0.07135961913200811,-7.69537,-32.790184,0.09970887488478153,-9.258622958144626 +35h-R,33.32177443154084,0.07073822911192638,6.156550027593463,0.07018811994943831,-7.7903075,-34.955532,0.09965073627388876,-8.91561112972059 +35t,32.33415553523643,0.07454452451026544,8.450029404768564,0.07020440202681734,-7.827303,-31.71143,0.10239894627585071,-9.11248958632706 +35l,31.645417047322635,0.07377141679618321,8.752487860435961,0.07092202912029053,-7.718495,-30.611425,0.10233355339601727,-9.70592871414551 +35q,35.053626955063855,0.07254220323397928,7.515000232032441,0.06945985830877453,-7.7659507,-35.304573,0.10043427286696006,-10.140580035694805 +35n,38.14661362031027,0.07340918271817384,8.705169436880423,0.07193268918967273,-7.7883954,-37.22984,0.10277752614948607,-9.74957000407174 +35r,36.74946796505808,0.07307326784051581,7.147007073308589,0.07151425137413925,-7.7560945,-37.358555,0.10224475841086104,-10.126213924596485 +35b,38.803650084587915,0.07314550089103669,8.184117725794954,0.06875482187334866,-7.6266108,-38.246147,0.10038670146705964,-7.885902864538171 +35m,42.75084678006913,0.07300689133217364,8.781375086920011,0.07078651627361143,-7.9436064,-41.91308,0.10168941473005963,-9.658749832281092 +19a-bindingpose1,33.74103617992892,0.07214774377648021,7.580100781744832,0.0708494740276779,-7.5574226,-33.718357,0.10111846963851483,-8.236320561638735 +35o,35.52228755652347,0.07074013816435917,8.428073501417776,0.06910892003871855,-7.5915995,-34.68581,0.0988949441398832,-9.226389986052087 +19a-bindingpose2,35.85587775618516,0.0855083187298201,7.6372085805719045,0.06912051591741342,-7.634033,-35.852703,0.10995143606470043,-8.236320561638735 +35k,43.278436395281894,0.06558019788405453,10.537682515485466,0.06802308785502323,-7.8313117,-40.572067,0.09448758032590293,-8.550876609667062 +19b,34.484987326580345,0.0758485661564554,6.631792568075828,0.07020925476187008,-7.892428,-35.74562,0.10335542773462537,-8.312530313121536 +19c-bindingpose1,31.595167332293894,0.07443917348961872,9.90492622259076,0.07259894129971801,-7.773734,-29.463974,0.10397979047708,-8.260657196280185 +19c-bindingpose2,36.83342557478018,0.07527898145905913,9.712580031482043,0.07315366329791005,-7.8261604,-34.947006,0.10496848814485879,-8.260657196280185 +19d-bindingpose1,,,9.96780445709426,0.07138601823008664,,,,-7.919978696712844 +19d-bindingpose2,35.91263491555635,0.07327241000584232,10.339576863059113,0.07352869466641812,-7.6363554,-33.209415,0.10380421478635445,-7.919978696712844 diff --git a/summaries/2026_jun_08_abfe/merck/pfkfb3/README.md b/summaries/2026_jun_08_abfe/merck/pfkfb3/README.md new file mode 100644 index 0000000..f981893 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/pfkfb3/README.md @@ -0,0 +1,33 @@ +# Pfkfb3 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.25 +- RMSE: 21.37 +- R²: 0.18 +- Kendall 𝜏: 0.26 +- Spearman ρ: 0.37 + +## System Details +- Ligands: 40 +- Host Atoms: 8158 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 36.93 Hours +- Average Time Per Molecule: 0.92 Hours +- Total Nanoseconds Simulated: 7102.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/pfkfb3/dg_plot.png b/summaries/2026_jun_08_abfe/merck/pfkfb3/dg_plot.png new file mode 100644 index 0000000..14d4087 Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/pfkfb3/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/pfkfb3/dg_results.csv b/summaries/2026_jun_08_abfe/merck/pfkfb3/dg_results.csv new file mode 100644 index 0000000..bd2405a --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/pfkfb3/dg_results.csv @@ -0,0 +1,41 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +43,35.055804338535204,0.07466485908675512,13.051364134415017,0.07473357585517659,-7.8255386,-29.82998,0.10564065762075903,-7.997660000000001 +30_flip_b,31.52813625760755,0.08026003954420668,8.530873523389081,0.07448402076974911,-7.7545967,-30.751862,0.10949677300115304,-9.19819 +65,38.14579229762459,0.07774114432830187,16.459143817675965,0.07777931930894941,-7.775758,-29.462404,0.10996957776420427,-9.4879 +49,38.543581401319685,0.083640717892134,18.70455160161938,0.0742468015851494,-7.7435665,-27.582596,0.11184076732183167,-7.93429 +24,31.906668466182598,0.07697759598991814,8.388585590826922,0.07303278086977597,-7.651416,-31.169497,0.10611002481367995,-8.86991 +67,45.86058398330193,0.07850114006222199,22.083194121073774,0.0774721705662018,-7.786233,-31.563622,0.1102921855949335,-10.2436 +62_flip,37.5296303638107,0.07449592605651371,15.730075140466166,0.07406853239805636,-7.748615,-29.54817,0.10505137072223038,-7.691739999999999 +56,39.9033105917649,0.07985311732621388,14.942632366559346,0.07982674993767407,-7.7733955,-32.734074,0.112910718500619,-10.5657 +59,38.60110070643767,0.07679959018364445,15.65860911077633,0.07604496058443543,-7.820464,-30.762959,0.10807873557117549,-8.11517 +38,33.92121380169296,0.07819085675368463,14.920046506343768,0.07835513611961592,-7.7488775,-26.750044,0.1106947940790296,-8.75876 +31,28.591066383012198,0.0783273035515218,9.012702899931764,0.07417803603246964,-7.7546606,-27.333025,0.10787746526168755,-9.28247 +48,36.986125254308625,0.07664065263154404,14.808445774640841,0.07645716619573845,-7.6869407,-29.86462,0.10825658362645557,-8.00636 +58,39.11809017285643,0.07635228581349617,14.856262247714687,0.07684010397106175,-7.739107,-32.000935,0.10832392684550071,-9.13315 +41,29.51995886081295,0.07741203438577798,11.33030862993461,0.07831110853132486,-7.7179303,-25.907581,0.1101147255690619,-7.38769 +29,31.811873504470363,0.07722867621913751,13.44837530180608,0.07839161805977256,-7.7880034,-26.1515,0.11004323792305293,-9.64602 +54,40.30090203469666,0.07897278893817672,13.703442549041949,0.08020586453122532,-7.767442,-34.364902,0.11255968238172616,-8.17959 +47,34.489949483713666,0.07667319120307503,12.448745868028881,0.07761045525900644,-7.715663,-29.756866,0.10909702569169126,-8.33345 +26,33.84604904316545,0.07575983885032615,11.76988143660198,0.07573811204700114,-7.785352,-29.861519,0.10712522951700727,-9.16944 +55,40.9772442090622,0.08123947595852174,14.49037459721309,0.07700469459823157,-7.864818,-34.35169,0.11193558613855625,-10.6355 +20,34.84290850140453,0.07658972216922884,14.516750537252,0.0753461497380299,-7.7379236,-28.064083,0.10743848389802085,-8.51645 +57,39.30659662145499,0.08116593195893121,16.07190556301221,0.07622549419430243,-7.712966,-30.947662,0.1113473595372943,-10.4744 +42,35.34566848533087,0.07993516829615817,13.201796061346904,0.07663651321988654,-7.798096,-29.94197,0.11073746560688923,-8.4668 +35,41.73860129219194,0.08042931239678383,15.752367839214092,0.07701333252202013,-7.772255,-33.758488,0.11135496252420314,-10.1388 +44,34.56340422936898,0.07454066553675694,13.408328603952473,0.07438055143354538,-7.6853046,-28.84038,0.10530326324583182,-9.94868 +63,40.71025452632017,0.0762725357291427,18.986081851827166,0.07686035533274052,-7.71613,-29.440304,0.10828210345402643,-8.56164 +69,36.71431773599549,0.08016279829887897,13.66978929409447,0.07671425441366476,-7.7177796,-30.76231,0.11095562654210574,-10.7146 +52,37.50435803697624,0.08238752030355802,14.677292516220591,0.07599057370443744,-7.732509,-30.559572,0.11208153636392894,-10.3953 +19,27.12220917617208,0.07515881261900946,7.622623583967923,0.07381490927480662,-7.897643,-27.39723,0.10534461517110073,-7.55079 +68,42.05402225650892,0.07532287206749197,18.736741665137842,0.07827477264430024,-7.7679152,-31.085196,0.10862999166442322,-9.77823 +33,29.822499898762253,0.08256809553193521,10.462474621733486,0.07322118649369663,-7.641825,-27.00185,0.11035774803481395,-8.60692 +70,40.5140648904257,0.07980725681322719,14.168244101137951,0.07455288750053216,-7.7793074,-34.12513,0.10921232199124511,-10.3039 +53,37.82302696818638,0.08158016327431826,13.950245154545602,0.07724565698993521,-7.7208033,-31.593586,0.11234862955849151,-6.99764 +64,41.578025089101274,0.07883871514317521,16.408623768751696,0.07556384530927451,-8.082526,-33.251926,0.1092036525183599,-9.42228 +39,36.06856010929005,0.07622873460395746,18.507076694810312,0.07501758908015099,-7.907119,-25.468603,0.10695073001489504,-7.1975 +37,40.158697494357746,0.08294042625041362,13.74146199746771,0.07985143403099716,-7.915245,-34.33248,0.11513194962045502,-9.99707 +23,35.26928962776357,0.07630717011691245,10.383696092701511,0.07324407623528544,-7.730195,-32.615788,0.10577087933269591,-7.914460000000001 +60_adjust,37.10008007379475,0.08036589112542733,13.578404513073421,0.07819479473564547,-7.756856,-31.27853,0.11212984607201497,-8.14374 +34,35.72320608480003,0.08062598040387746,14.230621280132285,0.07408189053420042,-7.730971,-29.223557,0.10949280899313747,-9.97238 +36,37.42516590548717,0.0800447897074954,13.655070301259316,0.07700884786448581,-7.7151833,-31.48528,0.11107443904307003,-7.44054 +46,31.087147836391605,0.07712780187618411,12.792047577885887,0.07541033394420671,-7.7397547,-26.034857,0.10786758682676036,-7.859360000000001 diff --git a/summaries/2026_jun_08_abfe/merck/shp2/README.md b/summaries/2026_jun_08_abfe/merck/shp2/README.md new file mode 100644 index 0000000..cbb1dc6 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/shp2/README.md @@ -0,0 +1,33 @@ +# Shp2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 26.79 +- RMSE: 27.00 +- R²: 0.01 +- Kendall 𝜏: 0.18 +- Spearman ρ: 0.26 + +## System Details +- Ligands: 26 +- Host Atoms: 8422 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 17.16 Hours +- Average Time Per Molecule: 0.66 Hours +- Total Nanoseconds Simulated: 4755.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/shp2/dg_plot.png b/summaries/2026_jun_08_abfe/merck/shp2/dg_plot.png new file mode 100644 index 0000000..72bc4ee Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/shp2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/shp2/dg_results.csv b/summaries/2026_jun_08_abfe/merck/shp2/dg_results.csv new file mode 100644 index 0000000..1f2b87d --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/shp2/dg_results.csv @@ -0,0 +1,27 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +SHP099-1 Example 7,51.841193668023045,0.08349884670809818,32.75409543492744,0.07543466155293087,-6.7703094,-25.857407,0.11252753247622425,-9.75265 +Example 22,60.86586892236593,0.08162077816327527,32.375947049997855,0.07430017888456415,-6.892646,-35.382565,0.11037421805048869,-9.23883 +Example 29,59.071072901486964,0.08592499214256022,29.238386680463876,0.07611828893808305,-6.9339943,-36.766678,0.11479154230848426,-7.62278 +11,56.888135914401474,0.08474258123550671,27.1211986253436,0.0780089913853192,-6.9062977,-36.67323,0.11518119556338725,-6.35409 +4,48.57207042090347,0.0805822015406518,22.040528112017572,0.07382762259697892,-7.1778693,-33.709415,0.10928865020421917,-5.82207 +Example 2,54.09221842928761,0.08399796968764955,29.011721947572056,0.07509989297603895,-6.9044633,-31.98496,0.11267498762662367,-8.27622 +Example 14,63.39878764745747,0.08006151276405814,30.574654437449553,0.0733890524044737,-6.892296,-39.71643,0.10860846577912805,-9.77823 +Example 26,63.20490249084951,0.08546646250946997,36.83000940187901,0.07623576495719593,-6.8806844,-33.255577,0.11452688798920305,-8.95905 +SHP836-2,48.53199177035235,0.08176799845753409,21.80596114731534,0.0756708291423722,-7.2427287,-33.968758,0.1114095146513321,-6.71321 +Example 6,63.43318547254622,0.08765658222448988,33.856385757524855,0.07669967929509793,-6.907049,-36.483845,0.11647539315773794,-9.06926 +Example 1,56.91208895529822,0.08267876838566918,29.577103083961607,0.07497229744965975,-6.9188123,-34.25379,0.11160924749612547,-8.98818 +3,49.0458956111377,0.07966914287591086,21.8992327777437,0.07211509145444608,-7.0804634,-34.227127,0.10746049851952771,-5.46294 +Example 9,66.63410575607246,0.08482021099134508,31.036047791559053,0.0745975117184624,-6.8110666,-42.40912,0.11295688092012116,-8.7941 +Example 8,59.843778794985354,0.08347097837696664,29.913373246228993,0.076365335888883,-6.8645625,-36.794964,0.11313296936185294,-9.71233 +7,49.11927009508051,0.08099761102831031,24.046157469385307,0.07364635339111898,-6.851852,-31.924969,0.10947327692228381,-7.07647 +Example 24,56.802107625733406,0.0838546450606168,29.195225755087456,0.07677246412734068,-6.96907,-34.57595,0.1136908648327817,-9.07722 +Example 28,71.58922776706339,0.08074990298594918,37.24499141900559,0.07486375033545917,-6.9291315,-41.27337,0.1101141587014593,-8.45735 +10,54.811278396753046,0.07940871058858463,25.598508800401486,0.07894741823084156,-6.7251205,-35.93789,0.11197516761611481,-7.15428 +Example 25,64.11669071844332,0.08463657275724278,36.358260631903015,0.07605818789927243,-6.8895025,-34.647934,0.11379014629840795,-8.86991 +Example 27,48.24974493874494,0.08055262809497477,20.13437727737687,0.07453924931713084,-7.1056743,-35.221046,0.10974892064056352,-8.51853 +6,64.6080929264985,0.08326082849417141,34.70717723044583,0.07352404577238554,-6.8399076,-36.740818,0.11107722929689806,-8.03004 +Example 30,63.72107434225742,0.08247554876066683,33.10970324551514,0.07561276082275271,-6.936675,-37.548042,0.1118905972037505,-9.1571 +Example 5,52.826539213540535,0.08160994650610953,29.457110437243827,0.07728601527179951,-7.1910286,-30.56046,0.11239800498817978,-7.56309 +Example 4,56.52366164015965,0.08022780310828084,29.779855067613777,0.07338234366496904,-7.0038104,-33.74762,0.10872657795288465,-8.20109 +Example 23,58.22405117365227,0.0861254884260201,32.32853196773748,0.07624827608075807,-6.8681645,-32.763683,0.11502781994764581,-8.74034 +Example 3,57.11843127953132,0.08149663996030454,30.285499737280414,0.07317935190306214,-6.9299793,-33.76291,0.10953045179205512,-8.21587 diff --git a/summaries/2026_jun_08_abfe/merck/syk/README.md b/summaries/2026_jun_08_abfe/merck/syk/README.md new file mode 100644 index 0000000..d586c84 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/syk/README.md @@ -0,0 +1,33 @@ +# Syk + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 22.13 +- RMSE: 22.22 +- R²: 0.04 +- Kendall 𝜏: 0.13 +- Spearman ρ: 0.19 + +## System Details +- Ligands: 46 +- Host Atoms: 4558 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 22.71 Hours +- Average Time Per Molecule: 0.49 Hours +- Total Nanoseconds Simulated: 8623.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/syk/dg_plot.png b/summaries/2026_jun_08_abfe/merck/syk/dg_plot.png new file mode 100644 index 0000000..02d23ba Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/syk/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/syk/dg_results.csv b/summaries/2026_jun_08_abfe/merck/syk/dg_results.csv new file mode 100644 index 0000000..115f2e7 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/syk/dg_results.csv @@ -0,0 +1,47 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3265014,41.778275721848644,0.08042220923683564,13.003210516232908,0.07613842089761333,-6.955625,-35.730694,0.11074651631232241,-10.4002 +CHEMBL3265036,39.90251827891528,0.08452739746838467,15.23645279962481,0.07527934944446976,-7.208762,-31.874826,0.11318949322070876,-10.4179 +CHEMBL3265020,35.857862646631,0.07964323752695472,11.526507566628183,0.07408724264182769,-7.071987,-31.403347,0.10877483535287,-11.0033 +CHEMBL3265023,36.35919932992165,0.08067194710689138,9.681478014291317,0.0752554696502744,-6.983394,-33.661114,0.11032383587557337,-10.4772 +CHEMBL3265033,47.35594442253179,0.08201768078247453,22.166559885731036,0.07768293738908985,-7.2313504,-32.420734,0.11296698067281938,-11.8386 +CHEMBL3265027,34.0447351065455,0.07426351285094619,11.84607141026631,0.07041476498867254,-7.1419396,-29.340605,0.10233918345078112,-10.3299 +CHEMBL3265028,34.83079143266595,0.07828971198311088,11.545413695282477,0.07188388075499166,-7.176221,-30.461597,0.10628532972520863,-11.0103 +CHEMBL3265032,38.22402304945415,0.0824508810542869,14.822345073916324,0.07622087550230065,-7.1252637,-30.52694,0.11228432503678056,-11.0688 +CHEMBL3265031,43.62524435148953,0.081190163922135,16.50621833898378,0.07775237695702811,-7.164949,-34.283974,0.11241563432268195,-12.0789 +CHEMBL3265037,40.34102003338243,0.08239363938804603,13.802476052981046,0.07631282326201001,-7.2564735,-33.79502,0.11230475860722085,-12.7646 +CHEMBL3265026,36.66514757551545,0.08077771312546242,11.418180368013305,0.07472526365797542,-7.135459,-32.382427,0.11004046513230233,-11.3613 +CHEMBL3265012,37.74331941280945,0.07900053319576131,12.052485369942936,0.07358627716829191,-7.0155754,-32.70641,0.10796306976324481,-10.5463 +CHEMBL3265029,35.17590259797177,0.07617423665637753,12.307423493435953,0.0713197643020092,-7.112114,-29.980593,0.1043504820797487,-11.1253 +CHEMBL3265035,42.58518442353265,0.07881426276423115,14.800492687795042,0.07544561338775786,-7.2503104,-35.035,0.1091042097928595,-11.0766 +CHEMBL3265024,38.25259592213751,0.08137750420950751,12.626310266038944,0.07427436720441981,-7.0269012,-32.653187,0.110177038510687,-11.7847 +CHEMBL3265018,43.539303848114834,0.07893196105652045,14.898347004672477,0.073987027408425,-7.1265335,-35.767487,0.1081865735706751,-11.1877 +CHEMBL3265008,39.76736525745706,0.08122353921733469,11.41429250606392,0.07404771510821798,-7.2211466,-35.57422,0.10991054287800474,-9.78436 +CHEMBL3265016,33.43379374562474,0.08152047937550377,10.88922482129662,0.07487387714781253,-7.3439617,-29.888533,0.1106873345815033,-11.6897 +CHEMBL3265025 flip,35.884665525130316,0.08175450349954543,13.398262455237235,0.07444680700910343,-6.9612617,-29.44766,0.11057181338979603,-10.1995 +CHEMBL3265013,36.47179053039113,0.08844423511697488,12.942415541851284,0.07540765644435832,-7.1352515,-30.664629,0.11622692190648906,-9.81322 +CHEMBL3259820,40.09136138859345,0.07880475944754452,14.169998049269443,0.07436514858338748,-7.226819,-33.148182,0.10835296689714895,-10.5757 +CHEMBL3265006,37.97007223065724,0.08060661784708979,12.712483776331679,0.07589055729111638,-7.341058,-32.598644,0.11071044904029155,-9.95804 +CHEMBL3265030_n,43.781349196264266,0.08236384003039812,17.850320695435855,0.07562093733503714,-7.1881647,-33.119194,0.11181381090000746,-11.4719 +CHEMBL3265022,35.9000645089348,0.07921719808899105,9.513733940448283,0.0748174241290771,-7.222313,-33.608643,0.10896334900497809,-10.7913 +CHEMBL3265019,40.6050112595836,0.07799068285799615,13.844452038394012,0.07400251137991411,-7.235529,-33.99609,0.10751240999619929,-10.777 +CHEMBL3265009,37.37690724915665,0.0815154612869741,12.296639960920988,0.07638319347651022,-7.2463813,-32.32665,0.11171017265449985,-10.2976 +CHEMBL3265021,38.41818910736356,0.07836713845159296,12.602840888493526,0.07295023752741449,-7.103911,-32.91926,0.10706608027007122,-10.8907 +CHEMBL3265005,40.6426366091987,0.08042777875962338,13.380433522336526,0.0736710355189425,-7.214505,-34.476707,0.10906901058797688,-10.3233 +CHEMBL3265017,38.67835076117707,0.07796192393656973,12.468050672631053,0.07251266626674367,-7.319647,-33.529945,0.10647134991632082,-11.4873 +CHEMBL3265010,37.357148977501424,0.07959836305258042,12.244975620403526,0.07680893150568696,-7.16651,-32.278683,0.11061424573578085,-10.1324 +CHEMBL3265034,35.38468226865501,0.08137044571724553,12.202045580818563,0.07500911860775013,-7.3626757,-30.545313,0.11066850188980931,-11.4873 +intermediate,28.752854681218246,0.07689843505558865,6.614394026977006,0.07195631238307565,-7.16064,-29.299099,0.105314197550802, +CHEMBL3265011 flip,38.08448252535642,0.08266742136484145,12.836400029407493,0.07616208290727268,-7.372214,-32.620293,0.11240358280716198,-8.63789 +CHEMBL3265015 flip,36.611560740111685,0.0825769379429022,13.32357683590801,0.07529382386128593,-7.2537875,-30.54177,0.11175021517509608,-9.47732 +CHEMBL3265002,46.7361700360319,0.08573156034025671,17.339403546401112,0.08059798202953423,-6.9571347,-36.3539,0.11766875178061591,-10.6173 +docked CHEMBL3264998,101.49262010277114,0.08918946395624036,74.83268080322654,0.085561790179937,-6.97057,-33.6305,0.12359441904712794,-11.7121 +CHEMBL3264997,103.94822276964673,0.09161663421683774,74.12088482933797,0.08563554366710704,-7.046063,-36.873398,0.12540755162422573,-10.983 +docked CHEMBL3264994,90.34310644012899,0.09269781612405532,66.6099312545135,0.08345962821931932,-7.5529237,-31.286097,0.12473329409855323,-9.80496 +CHEMBL3264995,101.91536726353907,0.09522055699871067,74.30189826038463,0.0825665916686301,-7.813182,-35.426647,0.12603252173514187,-12.3815 +docked CHEMBL3265004,43.38693350291492,0.08618842537581752,17.003508603981608,0.08206171466124808,-7.02214,-33.405567,0.11900659511937547,-10.8575 +CHEMBL3265001,90.07620044155588,0.09283837167048792,64.26463430964759,0.08426922719428508,-7.257166,-33.06873,0.12538048455142325,-12.038 +CHEMBL3264996,38.49802772756041,0.08691846960115014,11.537239167776752,0.08071582386938785,-6.908276,-33.869064,0.11861645999067795,-10.6659 +intermediate_1,34.354473599279714,0.08121895993367687,10.418199057765401,0.07801055958313552,-6.9984922,-30.934767,0.11261512713300174, +docked CHEMBL3264999 adjust,47.26773167230258,0.08493318774174369,17.927159686914095,0.08035245855325812,-6.948731,-36.289303,0.11691947645934507,-11.414 +redocked CHEMBL3265000 ground state,92.45531460250488,0.09546322347887615,66.13569109742751,0.08599188772887335,-7.540095,-33.85972,0.1284828073796374,-11.8111 +CHEMBL3265003 tautomer 2,44.20752624280969,0.0876186009013261,15.654003857655066,0.07932154222419076,-7.348033,-35.901558,0.11819021230512254,-10.821 diff --git a/summaries/2026_jun_08_abfe/merck/tnks2/README.md b/summaries/2026_jun_08_abfe/merck/tnks2/README.md new file mode 100644 index 0000000..6e4f0ab --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/tnks2/README.md @@ -0,0 +1,33 @@ +# Tnks2 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 24.44 +- RMSE: 24.53 +- R²: 0.13 +- Kendall 𝜏: 0.21 +- Spearman ρ: 0.32 + +## System Details +- Ligands: 27 +- Host Atoms: 4097 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 9.99 Hours +- Average Time Per Molecule: 0.37 Hours +- Total Nanoseconds Simulated: 4529.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/merck/tnks2/dg_plot.png b/summaries/2026_jun_08_abfe/merck/tnks2/dg_plot.png new file mode 100644 index 0000000..e060e05 Binary files /dev/null and b/summaries/2026_jun_08_abfe/merck/tnks2/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/merck/tnks2/dg_results.csv b/summaries/2026_jun_08_abfe/merck/tnks2/dg_results.csv new file mode 100644 index 0000000..3929c32 --- /dev/null +++ b/summaries/2026_jun_08_abfe/merck/tnks2/dg_results.csv @@ -0,0 +1,28 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a,31.13264040778738,0.06665384950596061,7.534989797899797,0.06499594338304344,-6.8661547,-30.463808,0.09309784267218567,-8.55056 +1b,35.517450194068374,0.07138353423712318,7.9360205143504245,0.06855373004559334,-6.84381,-34.42524,0.0989708182412706,-9.93717 +3a,32.875622132965695,0.07263398344728933,4.662066159557252,0.0697107543326529,-7.025398,-35.238953,0.100674151702652,-10.9965 +3b,30.760404966965943,0.07280082028092293,3.449563542684249,0.06837811229914004,-6.994607,-34.30545,0.09987755341000822,-11.5193 +5f,39.31981679201354,0.07513260741024876,10.255364927147495,0.06939278868776026,-6.902183,-35.966637,0.10227545071094389,-10.2631 +5l,34.63571134569855,0.07430612393281645,10.099799835726786,0.07145589478961246,-7.010734,-31.54665,0.10308901471108957,-10.0926 +5g,34.55153640817212,0.08246084063072791,10.622822169863744,0.06999069714818279,-6.8962636,-30.824978,0.10815954846806151,-10.806 +5e,37.85791323551298,0.07305312121843201,9.420874959427342,0.06955865866995438,-7.026004,-35.46304,0.10087202543677876,-10.1076 +5i,38.54493178740474,0.07604092520637121,9.861926016921178,0.06924144242622723,-7.1730347,-35.856037,0.1028425965031294,-12.0789 +5b,37.08931803979562,0.07269331909491758,10.625912495475962,0.07076948312881601,-7.072185,-33.53559,0.10145264108615054,-10.4744 +5h,39.26838679051131,0.08110475278722937,11.187548175704313,0.07217195523192514,-6.9697957,-35.050636,0.10856690124838507,-10.0498 +5a,38.089485830652386,0.07868440212701741,10.4773976145879,0.07038469190636733,-6.921707,-34.533794,0.10557101871650397,-10.7585 +5k,37.19198536271907,0.07337873817960684,8.650951685958841,0.07023731691357141,-6.98906,-35.530094,0.1015761778373687,-10.9634 +5p,33.39222525681643,0.07723932407410884,6.292726382689113,0.07267120794731688,-6.913403,-34.0129,0.10605195730370742,-10.5033 +5j,36.76291810056046,0.07479448114154483,9.70598098871617,0.07026627005620492,-6.9742513,-34.031193,0.10262340433275649,-11.0844 +5d,38.57619580018255,0.0717216526365894,9.373274363637332,0.06852545075494651,-6.9824266,-36.18535,0.0991954276067813,-10.8851 +5m,38.297841267420104,0.07971983206995527,8.207180992375726,0.07029450984658012,-6.9885674,-37.079227,0.10628532231607908,-12.6889 +5n,40.15850988710884,0.08218583531934398,7.937284788205665,0.07237646262383116,-6.9042687,-39.125496,0.109511934824827,-10.7146 +5c,40.46542614874893,0.07401047086731953,10.41431361794719,0.06871844516983919,-6.963693,-37.014805,0.10099393300868398,-9.96041 +7,38.32532313773581,0.07248609112279132,8.14142018754659,0.06872110037239318,-7.075042,-37.25894,0.09988404798892636,-8.39681 +8c_adjust,59.083701754586855,0.07947976064758443,30.157573304344343,0.07338398931480464,-6.923223,-35.84935,0.10817690252707679,-10.123 +8d,58.00559389255649,0.07815763337067202,29.308237931467595,0.07433164104326831,-6.983585,-35.680943,0.10786013403611956,-12.4895 +5o_adjust,39.53247595776774,0.0771945536644902,6.958954112637989,0.0742606972587999,-6.9285474,-39.50207,0.10711512625592609,-12.038 +8f,54.08764627815938,0.08145258706356485,23.327782334235103,0.07538268300396737,-7.004099,-37.763966,0.11098230866324707,-11.8111 +8b,56.713388765495885,0.0788555094122057,26.427803837360187,0.07466675401193781,-7.12956,-37.415146,0.1085970327372608,-11.93 +8e,52.663196693802206,0.07996484290988964,24.75491509063002,0.07553042642793766,-6.943558,-34.85184,0.10999646093392929,-10.2436 +8a,51.984709185094964,0.0788256220965507,27.260012063532265,0.07321885764303508,-6.955203,-31.679901,0.1075847564177159,-10.806 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/btk/README.md b/summaries/2026_jun_08_abfe/miscellaneous_set/btk/README.md new file mode 100644 index 0000000..e754c69 --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/btk/README.md @@ -0,0 +1,33 @@ +# Btk + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 15.93 +- RMSE: 16.04 +- R²: 0.20 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.31 + +## System Details +- Ligands: 6 +- Host Atoms: 5400 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.44 Hours +- Average Time Per Molecule: 0.41 Hours +- Total Nanoseconds Simulated: 962.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/btk/dg_plot.png b/summaries/2026_jun_08_abfe/miscellaneous_set/btk/dg_plot.png new file mode 100644 index 0000000..f643165 Binary files /dev/null and b/summaries/2026_jun_08_abfe/miscellaneous_set/btk/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/btk/dg_results.csv b/summaries/2026_jun_08_abfe/miscellaneous_set/btk/dg_results.csv new file mode 100644 index 0000000..6b06dfc --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/btk/dg_results.csv @@ -0,0 +1,7 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2,29.004476809997495,0.06867062929251591,12.160148207175622,0.06065064039550247,-6.931213,-23.77554,0.09161962403227104,-7.687929999999999 +7,29.40473382903741,0.07561379554201714,14.59491576307983,0.06884129255715035,-7.061309,-21.871126,0.10225736959852397,-9.08461 +8,31.58973368422465,0.07264062726921688,13.296417361178937,0.06975924634762021,-7.1701818,-25.4635,0.10071252742858387,-9.60639 +9 flip,36.4235447043086,0.07387192539563955,16.095668164069327,0.07049090450331727,-7.2486725,-27.57655,0.10210792809255671,-8.33091 +10,37.88090751504289,0.07792239667840947,18.240805561494053,0.06886041262683594,-7.1598854,-26.799986,0.10398873175130806,-10.8701 +11,36.99040852566161,0.07816106551355159,16.97878842542546,0.06969697975439977,-7.1980104,-27.20963,0.1047225913979353,-11.5248 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/README.md b/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/README.md new file mode 100644 index 0000000..aad1864 --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/README.md @@ -0,0 +1,33 @@ +# Cdk8 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 25.69 +- RMSE: 25.76 +- R²: 0.17 +- Kendall 𝜏: 0.16 +- Spearman ρ: 0.27 + +## System Details +- Ligands: 10 +- Host Atoms: 11038 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 8.04 Hours +- Average Time Per Molecule: 0.80 Hours +- Total Nanoseconds Simulated: 1517.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/dg_plot.png b/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/dg_plot.png new file mode 100644 index 0000000..9c3ec5d Binary files /dev/null and b/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/dg_results.csv b/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/dg_results.csv new file mode 100644 index 0000000..831a71d --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/cdk8/dg_results.csv @@ -0,0 +1,11 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12,28.901790678198513,0.0686795962613841,0.40668904361466,0.06783965479177338,-7.698269,-36.19337,0.09653551525160937,-9.83296 +13,33.912269935638946,0.07127630145647881,5.593806343198551,0.06812989898962,-7.027831,-35.346294,0.09860017386217262,-11.1972 +14,34.851562545848545,0.0728965976499564,3.895864148358729,0.0681550826346478,-7.677215,-38.63291,0.09979493593301865,-11.0316 +15,32.26458712007725,0.07226011855076321,3.1008909536692175,0.06852598847822354,-7.666371,-36.830067,0.09958582143000065,-9.72018 +16,31.446118012320344,0.0742328159876488,3.2306607306189963,0.06897373517273638,-7.4099483,-35.625404,0.10133058330600342,-10.6355 +17,27.956595648415654,0.07419171128711124,2.900945966139067,0.06925285757353011,-7.357657,-32.413307,0.10149073014718989,-10.3953 +19,28.525591186115932,0.0731604364297552,1.242011072184456,0.06798067727121465,-7.0742917,-34.35787,0.09986902393057265,-10.2248 +20,29.626224385366704,0.07608657344037144,0.3914529924858561,0.06674335579259674,-7.66139,-36.896164,0.10121186788294244,-10.2831 +21,26.83058224616825,0.07292388855030327,-0.4007851330550669,0.06925997703404671,-7.812547,-35.043915,0.10057255062915392,-9.86234 +22,35.62720534296628,0.0683194492294815,3.2213511914044406,0.06879105614139962,-7.666489,-40.072342,0.0969523416327264,-11.2901 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/faah/README.md b/summaries/2026_jun_08_abfe/miscellaneous_set/faah/README.md new file mode 100644 index 0000000..ae89ae2 --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/faah/README.md @@ -0,0 +1,33 @@ +# Faah + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 27.01 +- RMSE: 27.14 +- R²: 0.30 +- Kendall 𝜏: 0.40 +- Spearman ρ: 0.56 + +## System Details +- Ligands: 24 +- Host Atoms: 8446 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 13.56 Hours +- Average Time Per Molecule: 0.57 Hours +- Total Nanoseconds Simulated: 4024.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/faah/dg_plot.png b/summaries/2026_jun_08_abfe/miscellaneous_set/faah/dg_plot.png new file mode 100644 index 0000000..7948a21 Binary files /dev/null and b/summaries/2026_jun_08_abfe/miscellaneous_set/faah/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/faah/dg_results.csv b/summaries/2026_jun_08_abfe/miscellaneous_set/faah/dg_results.csv new file mode 100644 index 0000000..bb77d7b --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/faah/dg_results.csv @@ -0,0 +1,25 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +6MRG ligand,37.09714392554775,0.07395139896846485,9.048325028435666,0.07272617497851443,-6.8256674,-34.87449,0.10372032557024954,-10.2873 +fig 3,35.30035234306751,0.07540884676374517,5.330957977440802,0.0733982254910028,-6.875618,-36.845013,0.1052320943223411,-10.5996 +2,34.390122702260996,0.07621020647704713,5.771124971559513,0.07163577362232283,-6.8913345,-35.51033,0.10459292344008193,-8.66521 +4,36.289418161855785,0.07620111371853246,5.265390382821895,0.07469260986661293,-6.936552,-37.960583,0.10670330688704432,-11.3247 +6,31.348077135222013,0.07482312476270041,5.5575017020151005,0.0726879269058639,-6.9206905,-32.71126,0.10431699150726523,-10.4205 +9,43.06490800891222,0.07406312938938493,6.836531234645439,0.07437985405794481,-6.8069577,-43.035336,0.104965279138532,-10.5657 +11,34.82976167367562,0.07521098460352967,5.665083611747514,0.07401292403730964,-6.8133593,-35.978035,0.10552063840588222,-12.1228 +12,35.144161910421154,0.07440838223011549,4.6927463679645856,0.07327331253754579,-6.9389,-37.390316,0.10442981220096027,-11.0462 +15,39.0892856606659,0.07631877793974884,9.77090158345282,0.07252425879317206,-6.707319,-36.025703,0.10528211614379572,-8.59027 +14,31.260282600534364,0.07458317482392608,6.314435365223725,0.07142264544921115,-6.832582,-31.77843,0.1032658910278706,-7.84252 +19,34.8908538281626,0.0739752704412007,7.859447940543602,0.0722836655650138,-6.8630815,-33.89449,0.10342760242973606,-7.972320000000001 +20,33.605315876641534,0.06880318446513474,7.342977000207262,0.07127631062146499,-6.8596153,-33.121952,0.0990665970362913,-6.82123 +22,34.74933366546148,0.07570528529446005,6.811622870753625,0.0734912210614552,-6.833199,-34.77091,0.10550947727393623,-9.97238 +23,38.82634813382537,0.07738296458193941,4.422457596362221,0.07232473341874839,-6.8628917,-41.26678,0.105919735043016,-10.6737 +24,36.2466223234521,0.0806637434044066,4.6612178713673185,0.07462935468472304,-6.7686768,-38.354084,0.10989167430096851,-11.6273 +25,38.485645015479875,0.07746356059503995,6.089526059307964,0.07398182169198955,-6.8702455,-39.266365,0.10711635337765547,-12.038 +26,36.41275768675151,0.07418123683949279,5.907460278887179,0.0727090511920463,-6.8147626,-37.32006,0.10387233522109982,-10.6737 +27,41.803149557496205,0.07524222804957717,5.696823665251663,0.07261205649016474,-6.7968073,-42.90313,0.10456530796394879,-11.1877 +28,39.86628226494001,0.07654250912970059,8.606083253212176,0.07331937416642628,-6.8125873,-38.07279,0.1059928598162476,-11.5891 +29,36.5865214357644,0.07280894556004927,4.786636608701468,0.07093771797146133,-6.81048,-38.610367,0.10165285231888382,-10.806 +30,32.85108129384696,0.07672347374537168,4.610274225411033,0.07485230620116866,-6.8220825,-35.062893,0.10718842832689661,-9.90394 +31,34.885849023352606,0.07400117457611817,4.704972183130504,0.07220648208520937,-6.8194113,-37.000286,0.10339221389334295,-11.2901 +33 (Saha 2018),36.289780546881715,0.0738515231720953,3.790673080813606,0.07160557677181667,-6.7961264,-39.295235,0.10286596181275447,-9.73619 +39,40.506714381250504,0.07187770208622422,3.694425736476875,0.07286172767552984,-6.8734574,-43.685745,0.1023485975334253,-10.7146 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/README.md b/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/README.md new file mode 100644 index 0000000..a8dd728 --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/README.md @@ -0,0 +1,33 @@ +# Galectin + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.64 +- RMSE: 21.67 +- R²: 0.38 +- Kendall 𝜏: 0.37 +- Spearman ρ: 0.50 + +## System Details +- Ligands: 26 +- Host Atoms: 2712 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 10.29 Hours +- Average Time Per Molecule: 0.40 Hours +- Total Nanoseconds Simulated: 4953.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/dg_plot.png b/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/dg_plot.png new file mode 100644 index 0000000..13d71ab Binary files /dev/null and b/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/dg_results.csv b/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/dg_results.csv new file mode 100644 index 0000000..64d4e0a --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/galectin/dg_results.csv @@ -0,0 +1,27 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +18a,34.02871911724624,0.08312912615440841,13.198657447671822,0.07720352735072182,-7.8348045,-28.664865,0.11344970802337573,-6.32775 +18b,28.467864197699488,0.0811590945920045,8.412231845704095,0.07860399460158524,-7.8203974,-27.876028,0.11298401038341654,-7.46041 +18d,31.42620761408543,0.08052931902857714,12.342576452888785,0.0785604008658737,-7.8032002,-26.886833,0.11250203468121422,-6.76476 +18e,30.353518636732414,0.0894295476706697,9.584825482642355,0.07808499849103816,-7.709917,-28.478611,0.11872199032161657,-6.47298 +18f,29.1152943185531,0.08877106848379346,8.740667278375401,0.07929978813421927,-7.8025556,-28.177181,0.11903259636707254,-5.53273 +18g,30.941717706879516,0.08626317598547882,11.302003759907619,0.07887028116375762,-7.7171674,-27.356882,0.11688394578363563,-6.47298 +18h,29.511334273937408,0.09009611044774281,8.87541804114984,0.07980809248648355,-7.7816725,-28.417587,0.12036046171456383,-5.99988 +18i,30.48427441426104,0.08745842921963688,9.473064797715343,0.07975369709962887,-7.827775,-28.838984,0.11836227879956344,-4.80608 +17m,26.563564134858925,0.08703286975738062,10.526227039374424,0.07793612279532358,-7.990981,-24.028318,0.11682790614648939,-4.10471 +17q,41.42778332461396,0.08345118902794103,22.645671517748358,0.0780259721047459,-7.8015847,-26.583696,0.11424602081940417,-4.98984 +17r,41.50850323859665,0.08502432671727136,24.948276810964508,0.07701113487262072,-7.816631,-24.37686,0.11471639389422195,-4.74961 +17n,30.473764487876366,0.07934813351626237,11.965779426346153,0.07620867555514277,-7.8198743,-26.327858,0.11001767368192993,-4.9141 +17p,29.586866671802152,0.08153355085811542,10.824615808505488,0.07683526936604289,-8.009093,-26.771345,0.1120329350418227,-5.04631 +17o,29.76660458828725,0.08239967601592417,10.218116736418667,0.07609570721755421,-7.9106703,-27.45916,0.11216177274129097,-5.10873 +17f,29.360954127962444,0.08324925160450428,8.842349875967084,0.07615139604901223,-7.959766,-28.478369,0.11282496626599794,-6.581 +17e,32.217151651401075,0.08136686608040034,10.416360812079166,0.07669609208980038,-7.762425,-29.563217,0.1118161769941762,-6.89697 +17g,31.787767556367243,0.08129064603239922,9.923800760941631,0.07796548884093511,-7.8027444,-29.666712,0.11263563637930404,-7.20868 +17a,29.116718408517002,0.08131768839115709,10.58423642787311,0.0782644599451454,-7.9369664,-26.46945,0.11286227064784136,-5.53273 +17j,31.781944229855444,0.08016046528086063,10.983946442971321,0.07604752295249333,-7.779673,-28.577673,0.1104940086215269,-6.44095 +17l,31.369167843903508,0.08300804745369178,10.042500742742298,0.07717758664482464,-7.8696694,-29.196337,0.11334335367543066,-5.94341 +17c,29.191926419579357,0.08283638081617403,10.40876661098408,0.0765233000082045,-7.947209,-26.730368,0.11277269807390383,-6.35409 +17k,29.416454520534224,0.08125918459707702,10.552481044523972,0.07760192001044469,-7.882345,-26.746319,0.11236152842805805,-6.62188 +17b,27.6398862984227,0.08087839484298578,10.263822496828093,0.07561236982471893,-7.930408,-25.30647,0.11071831475816446,-5.50639 +17h flip,29.874980373021124,0.08085947247812456,8.77006721493305,0.07714690096518047,-7.768445,-28.873358,0.11175821499098823,-6.32775 +17i,29.537074644161798,0.08411584681042586,9.537330277951437,0.0763077390938856,-7.8816724,-27.881418,0.11357088856857442,-5.94341 +17d,31.569029263120328,0.08175649577258598,10.254502827133743,0.0759260733654068,-7.8933907,-29.20792,0.11157460830180856,-6.1509 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/README.md b/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/README.md new file mode 100644 index 0000000..ba00dc3 --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/README.md @@ -0,0 +1,33 @@ +# Hiv1 Protease + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 24.76 +- RMSE: 25.21 +- R²: 0.53 +- Kendall 𝜏: -0.58 +- Spearman ρ: -0.73 + +## System Details +- Ligands: 13 +- Host Atoms: 3626 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 7.31 Hours +- Average Time Per Molecule: 0.56 Hours +- Total Nanoseconds Simulated: 2948.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/dg_plot.png b/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/dg_plot.png new file mode 100644 index 0000000..1d178c6 Binary files /dev/null and b/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/dg_results.csv b/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/dg_results.csv new file mode 100644 index 0000000..274488f --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/hiv1_protease/dg_results.csv @@ -0,0 +1,14 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1,26.0964895031873,0.09421479613452574,6.9015247416105865,0.08670070475934265,-7.2344456,-26.42941,0.12803686975413348,-11.7595 +9,41.758759281414086,0.10030141328613752,7.2657431141854465,0.08603261363990616,-7.298252,-41.791267,0.1321438009023122,-10.5033 +10,39.15737685922435,0.09564379405813533,9.96155734093316,0.08747393653205611,-7.303419,-36.499237,0.1296125955077252,-10.806 +11 (2cen),37.972796785009336,0.09554595836594602,9.285863470101804,0.08861158683582573,-7.271117,-35.95805,0.13031133289791097,-11.3247 +12,42.56740647529907,0.0964581549595798,10.709392742901043,0.088018869355253,-7.286427,-39.14444,0.130581380835031,-11.2682 +13,32.17375987564241,0.09963459337279788,6.190167411452179,0.08903465689419902,-7.300499,-33.284092,0.13361969287807288,-10.8575 +14,40.104471968482194,0.09840433429741656,6.559745976150366,0.08915420012994787,-7.235656,-40.780384,0.13278510612763958,-10.6737 +15,41.563409137084506,0.09996621452282779,11.280320882619495,0.08941912817258897,-7.394781,-37.677868,0.13412316924815756,-10.9764 +16,41.30986224824616,0.09943390679936066,9.897527071086579,0.08904138140953399,-7.3527203,-38.765057,0.1334746021709825,-11.0612 +17,28.73176828144407,0.10079499337103122,7.995850994050747,0.08824297049622704,-7.278421,-28.014341,0.1339643703775904,-11.4873 +18,38.990094912060215,0.10154430692004725,12.782757259752598,0.0849793851393344,-7.274965,-33.4823,0.13241126147927176,-11.8386 +19,41.28697771756272,0.09613129981905102,9.319135459997797,0.0880203863238028,-7.4390893,-39.406933,0.13034114934851454,-10.8575 +20,35.77910151917242,0.09871845587544228,7.65574928613953,0.09071123975454723,-7.444377,-35.567734,0.13406663473153413,-11.536 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/README.md b/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/README.md new file mode 100644 index 0000000..026e967 --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/README.md @@ -0,0 +1,33 @@ +# Malt1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 28.65 +- RMSE: 28.77 +- R²: 0.26 +- Kendall 𝜏: 0.38 +- Spearman ρ: 0.52 + +## System Details +- Ligands: 16 +- Host Atoms: 6224 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 11.17 Hours +- Average Time Per Molecule: 0.70 Hours +- Total Nanoseconds Simulated: 2678.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/dg_plot.png b/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/dg_plot.png new file mode 100644 index 0000000..948bf76 Binary files /dev/null and b/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/dg_results.csv b/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/dg_results.csv new file mode 100644 index 0000000..8cbb98b --- /dev/null +++ b/summaries/2026_jun_08_abfe/miscellaneous_set/malt1/dg_results.csv @@ -0,0 +1,17 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +Pfizer-01-13,37.84898851030861,0.07439703194374915,14.705820762180734,0.06995142427305313,-7.762848,-30.906013,0.10211816743296914, +Pfizer-01-12,40.255983199808206,0.07383034267997533,12.711786153012453,0.06992870023609322,-7.6762967,-35.220493,0.10169042539468487, +Pfizer-01-05,38.44720217593219,0.07608439018735073,13.794568583897169,0.06972691283185993,-7.792676,-32.44531,0.10320211627308243,-6.671495008018873 +Pfizer-01-04,37.34196593607214,0.07867754081574133,12.326734304483766,0.07136012750890125,-7.800819,-32.81605,0.10621875176681041,-7.187253218618596 +Pfizer-01-01,37.901715513844145,0.07833465012633557,11.78957461900935,0.07218279790336843,-7.8729115,-33.985054,0.10652076663061497,-8.845471319203405 +1832576-04-1,39.52516154113464,0.07476447880113328,7.373298591095591,0.07327661565983823,-7.837136,-39.989,0.1046861485248395,-10.031196069300446 +1832577-09-9,39.75093733298271,0.07597114036213232,7.812737877006475,0.07355571858374,-7.7895927,-39.72779,0.1057452500318249,-8.385343719764283 +Pfizer-01-07,40.20907830336622,0.07627670979062035,10.079029215554833,0.07298198760161322,-7.80904,-37.93909,0.10556754695816581,-6.463477018541003 +Pfizer-01-03,37.16642686661973,0.07690741518441306,11.244312604692206,0.07246082017528606,-7.858882,-33.781,0.10566608240501223,-8.323545811509687 +2714550-01-1,43.39382153720969,0.07780828765427858,10.441056069453072,0.07497852628455273,-7.7802973,-40.733063,0.10805512033908585,-8.771566645289406 +Pfizer-01-09,36.77503972160273,0.07939924500763638,9.957524829428566,0.07210645139122611,-7.7927985,-34.61031,0.10725474553612034, +Pfizer-01-02,42.032494293010956,0.07679338161052561,10.472298014923872,0.07357473579152995,-7.8542795,-39.414474,0.10635067092394504,-8.584573845890262 +Pfizer-01-11,35.161308269742115,0.07608091019053817,13.734243645647537,0.07119524009922489,-7.777723,-29.204786,0.10419725096281099, +Pfizer-01-06,39.546887428540025,0.08099271442063725,11.80512905097107,0.07571626747769737,-7.797878,-35.539635,0.11087277821889877,-6.6378646965251065 +Pfizer-01-10,36.14203840888669,0.0782113798121247,12.22083982145503,0.07343568133521607,-7.8608527,-31.782051,0.10728382555298739, +Pfizer-01-08,40.90754047364299,0.07824729636227669,10.71817886424691,0.0716016906748355,-7.751731,-37.941093,0.10606338432984676, diff --git a/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/README.md b/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/README.md new file mode 100644 index 0000000..f4209d0 --- /dev/null +++ b/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/README.md @@ -0,0 +1,33 @@ +# Bace1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 23.81 +- RMSE: 23.96 +- R²: 0.64 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 6106 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.74 Hours +- Average Time Per Molecule: 0.58 Hours +- Total Nanoseconds Simulated: 540.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/dg_plot.png b/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/dg_plot.png new file mode 100644 index 0000000..f149c69 Binary files /dev/null and b/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/dg_results.csv b/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/dg_results.csv new file mode 100644 index 0000000..52b9523 --- /dev/null +++ b/summaries/2026_jun_08_abfe/scaffold_hopping_set/bace1/dg_results.csv @@ -0,0 +1,4 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +31,43.7533272927247,0.07812431660874523,16.34572386887623,0.07073462551606216,-7.1360583,-34.54366,0.10538878542084551,-8.35 +7,41.255246943299525,0.0804974502686719,20.357321057719723,0.0745709009149749,-6.9005914,-27.798515,0.10972993558290423,-7.71 +6,47.07420124924948,0.07935559033000429,21.11160511652921,0.071542647074063,-7.0058117,-32.968407,0.10684409233545579,-7.829999999999999 diff --git a/summaries/2026_jun_08_abfe/scaffold_hopping_set/factor_xa/dg_results.csv b/summaries/2026_jun_08_abfe/scaffold_hopping_set/factor_xa/dg_results.csv new file mode 100644 index 0000000..b9e27b9 --- /dev/null +++ b/summaries/2026_jun_08_abfe/scaffold_hopping_set/factor_xa/dg_results.csv @@ -0,0 +1,4 @@ +mol,solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol) +Edoxaban,35.385474677212734,0.08350664460156554 +4d,35.47614022679061,0.08361432978219586 +4c,35.818297348654674,0.08318683865929156 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/README.md b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/README.md new file mode 100644 index 0000000..16ce3e5 --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/README.md @@ -0,0 +1,33 @@ +# 2Ep9 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.30 +- RMSE: 21.40 +- R²: 0.76 +- Kendall 𝜏: -0.67 +- Spearman ρ: -0.80 + +## System Details +- Ligands: 4 +- Host Atoms: 4374 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.74 Hours +- Average Time Per Molecule: 0.43 Hours +- Total Nanoseconds Simulated: 674.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/dg_plot.png b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/dg_plot.png new file mode 100644 index 0000000..6c53c00 Binary files /dev/null and b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/dg_results.csv b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/dg_results.csv new file mode 100644 index 0000000..847fcaa --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/2EP9/dg_results.csv @@ -0,0 +1,5 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +ligand_5,33.70162645216484,0.07758932473722126,10.649102083863902,0.07013548453345705,-6.883216,-29.935738,0.10459010232292903,-11.18 +ligand_7,35.63917098407996,0.07702771638402799,7.744758794827152,0.07265493637252389,-6.859538,-34.75395,0.10588677382295557,-10.27 +ligand_4,32.8787279673312,0.0788518877821127,8.676471126101717,0.07156101660545407,-7.2100587,-31.412313,0.10648285920470472,-10.88 +ligand_6,34.22885325080171,0.07647791408481179,8.571594093218836,0.07098358760654286,-6.8545523,-32.51181,0.10434338049085624,-11.09 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/README.md b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/README.md new file mode 100644 index 0000000..b6c52d7 --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/README.md @@ -0,0 +1,33 @@ +# 3Rkz + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 35.34 +- RMSE: 35.44 +- R²: 0.38 +- Kendall 𝜏: 0.52 +- Spearman ρ: 0.64 + +## System Details +- Ligands: 7 +- Host Atoms: 3289 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.32 Hours +- Average Time Per Molecule: 0.47 Hours +- Total Nanoseconds Simulated: 1359.20 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/dg_plot.png b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/dg_plot.png new file mode 100644 index 0000000..8fa262b Binary files /dev/null and b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/dg_results.csv b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/dg_results.csv new file mode 100644 index 0000000..d838881 --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/3RKZ/dg_results.csv @@ -0,0 +1,8 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +lignad_63,51.872595231184384,0.08219550632078236,15.29760720390445,0.0783370228326568,-7.488495,-44.063484,0.1135464240106837,-9.32 +ligand_69,66.33677878517686,0.09412742556955873,26.080093520084333,0.08279255315107582,-8.025253,-48.281937,0.12535780431080681,-13.14 +ligand_62,55.03222061599815,0.08329130290736066,23.782983358380356,0.07800522926938233,-7.4789023,-38.72814,0.11411510387926135,-6.67 +lignad_65,57.44492443918389,0.08259751684457153,15.006797786843306,0.07839986457628677,-7.5238523,-49.961983,0.11388102807083093,-9.28 +lignad_68,51.29178821797426,0.0863367460222635,13.451807894293603,0.07949600350833468,-7.346319,-45.1863,0.11736118731296984,-8.45 +ligand_64,56.07959049342311,0.08567506292647668,19.876731103579257,0.08239506107808393,-7.7847695,-43.987633,0.11886615370876993,-8.89 +ligand_70,72.55431457223317,0.09009242517782776,34.74624251635743,0.08471763971368107,-7.8739023,-45.681973,0.12366779513308856,-12.74 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/README.md b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/README.md new file mode 100644 index 0000000..e81677d --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/README.md @@ -0,0 +1,33 @@ +# Mht1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 24.61 +- RMSE: 24.83 +- R²: 1.00 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 2487 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.01 Hours +- Average Time Per Molecule: 0.34 Hours +- Total Nanoseconds Simulated: 508.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/dg_plot.png b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/dg_plot.png new file mode 100644 index 0000000..d1e2d3f Binary files /dev/null and b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/dg_results.csv b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/dg_results.csv new file mode 100644 index 0000000..de6227b --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/MHT1/dg_results.csv @@ -0,0 +1,4 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +5AN26_ligand,36.556929023976274,0.07747822772273512,14.680421358977375,0.07028846315210058,-7.251506,-29.128014,0.10461043840525765,-7.57 +5ANT_A_ligand,37.46164879464587,0.07856747013511092,13.130263843767283,0.0727701963203146,-7.3115826,-31.642965,0.10709037695296751,-8.55 +5ANU_ligand,49.777803213617176,0.07546600161542404,14.807632938428638,0.07344424638935876,-7.159362,-42.12953,0.10530515052702798,-12.96 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/README.md b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/README.md new file mode 100644 index 0000000..d2865f0 --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/README.md @@ -0,0 +1,33 @@ +# Hsp90 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 19.29 +- RMSE: 19.44 +- R²: 0.13 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.48 + +## System Details +- Ligands: 10 +- Host Atoms: 3366 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.13 Hours +- Average Time Per Molecule: 0.41 Hours +- Total Nanoseconds Simulated: 1764.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/dg_plot.png b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/dg_plot.png new file mode 100644 index 0000000..c8999ad Binary files /dev/null and b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/dg_results.csv b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/dg_results.csv new file mode 100644 index 0000000..7752815 --- /dev/null +++ b/summaries/2026_jun_08_abfe/schrodinger_macrocycles/hsp90/dg_results.csv @@ -0,0 +1,11 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +lig_3B27,26.61644052695175,0.06677462850344082,5.541104103441305,0.06504189984302693,-8.066059,-29.141396,0.09321641350622152,-7.04 +18 minimized,43.091721365761146,0.08179590673422894,17.278505438911456,0.07699939338595525,-7.73286,-33.546074,0.11233644528949528,-13.1773 +"8, 3VHA",23.809841742850487,0.07811203887405666,5.938401554794112,0.07265718624977419,-7.853446,-25.724886,0.10667969502579444,-10.1525 +13,31.597675508638893,0.08632980567055956,9.783469758455178,0.07670471496969132,-7.6077714,-29.42198,0.11548354274829883,-11.2636 +9,26.60899203908776,0.07712857598106716,5.187774345025167,0.07345767545736563,-7.860131,-29.281347,0.10651219327601374,-9.7103 +"16, 3VHD",43.47572543504056,0.07835139209790468,17.45105723763793,0.07569467800478481,-7.5647264,-33.589394,0.10894321879735173,-12.7408 +"11, 3VHC",32.56221944094971,0.07818759962323571,10.93666716604463,0.07653140519373663,-7.2555256,-28.881077,0.10940912537705119,-12.1947 +12,31.380946337160562,0.08025826652801044,9.33076034374709,0.07614954595867084,-7.57896,-29.629147,0.11063517838279505,-11.1582 +7,32.59803650689626,0.07779453470686297,6.6270688154591255,0.07282858196622548,-7.350319,-33.321285,0.10656449681516134,-9.49772 +"17, top conformer",37.95345048037751,0.079733780880107,15.626782846526881,0.07486053052271578,-7.897729,-30.224398,0.10936898483381555,-12.9277 diff --git a/summaries/2026_jun_08_abfe/water_set/brd4/README.md b/summaries/2026_jun_08_abfe/water_set/brd4/README.md new file mode 100644 index 0000000..fc8cd2f --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/brd4/README.md @@ -0,0 +1,33 @@ +# Brd4 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 22.14 +- RMSE: 22.36 +- R²: 0.01 +- Kendall 𝜏: 0.21 +- Spearman ρ: 0.02 + +## System Details +- Ligands: 8 +- Host Atoms: 2499 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.94 Hours +- Average Time Per Molecule: 0.37 Hours +- Total Nanoseconds Simulated: 1374.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/brd4/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/brd4/dg_plot.png new file mode 100644 index 0000000..923aab7 Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/brd4/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/brd4/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/brd4/dg_results.csv new file mode 100644 index 0000000..55e638e --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/brd4/dg_results.csv @@ -0,0 +1,9 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 5 (1-Butenyl),33.0725758863409,0.08046480186648976,9.615443421174149,0.07328892915448378,-7.251897,-30.709028,0.10883864881568676,-7.64 +cmpd 2 (methyl),32.039112830695366,0.07673562277953937,11.783837787252384,0.07054169835264297,-6.7555566,-27.010832,0.10423284995546765,-9.59 +cmpd 3 (Allyl),32.39674461202864,0.08560604246955993,9.948297246438457,0.07190659915494521,-6.8127127,-29.26116,0.11179871872848127,-7.09 +cmpd 9 (methoxyethyl),34.628756284549745,0.07840767743508721,11.159765039531795,0.07371428295583471,-7.1636586,-30.63265,0.10761765372120667,-7.22 +cmpd 6 (ethyl),30.257691619141074,0.07963968401846902,10.650406107326022,0.07123480614894322,-6.7822657,-26.389555,0.10684978651190234,-8.59 +cmpd 8 (n-Butyl),34.41581983477027,0.0799479177566622,8.740084475280472,0.07261281068875666,-7.2350154,-32.91075,0.10800134179605009,-7.660000000000001 +cmpd 7 (n-propyl),31.025596620723718,0.08277953980994525,9.914464034268281,0.07312085150063295,-6.7322116,-27.843344,0.11044958639725153,-7.02 +cmpd 4 (Crotyl),37.69596244604,0.07801883109963716,9.078696771339738,0.07267419380048916,-7.1735597,-35.790825,0.1066230577816298,-8.64 diff --git a/summaries/2026_jun_08_abfe/water_set/chk1/README.md b/summaries/2026_jun_08_abfe/water_set/chk1/README.md new file mode 100644 index 0000000..3f22916 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/chk1/README.md @@ -0,0 +1,33 @@ +# Chk1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 28.21 +- RMSE: 28.36 +- R²: 0.00 +- Kendall 𝜏: 0.04 +- Spearman ρ: 0.01 + +## System Details +- Ligands: 13 +- Host Atoms: 4834 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 6.47 Hours +- Average Time Per Molecule: 0.50 Hours +- Total Nanoseconds Simulated: 2442.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/chk1/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/chk1/dg_plot.png new file mode 100644 index 0000000..1a06d7a Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/chk1/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/chk1/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/chk1/dg_results.csv new file mode 100644 index 0000000..15ab8a5 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/chk1/dg_results.csv @@ -0,0 +1,14 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +21 (Xtal),56.464351345042665,0.08457832305832452,27.43849669325818,0.07970341913441495,-6.9248557,-35.950706,0.11621586704522982,-13.0686 +22,60.93711461997593,0.08478286443758293,30.4507173843056,0.08048091331789177,-7.0732718,-37.55967,0.11689872330664512,-13.0686 +24 pose 2,53.837418796735825,0.08564264311106501,18.052772409263774,0.0809272743851091,-6.8934736,-42.67812,0.11782990307410078,-13.1773 +14 docked,49.6919908274536,0.08089571595762396,18.313055926924008,0.0760531886341302,-7.00828,-38.387215,0.11103244733732191,-10.8701 +18 docked,48.4646525841813,0.08347632988132093,18.22964046121176,0.07774611040353112,-7.047824,-37.282837,0.11407346463281094,-9.54958 +13 docked,56.7641532199015,0.08162680350738476,26.000382048517714,0.07688785164396142,-6.969282,-37.733055,0.11213686628962403,-9.92085 +20,52.360013133037185,0.08258821719600279,15.498001356167325,0.07633252128019173,-6.9894643,-43.851475,0.11246095955755071,-10.0823 +12 docked,54.637752170354965,0.08150913077600076,23.004884991921674,0.07888495188055908,-6.945801,-38.578667,0.11343092185580314,-8.61243 +16 docked,55.41377733670659,0.08072407534211928,21.18101128288736,0.07657599262322541,-6.966732,-41.1995,0.11126661218026018,-11.7816 +19,51.5238105082299,0.08319967387181022,18.549193418542853,0.07627149997028966,-6.9336,-39.90822,0.11286951510524655,-10.2494 +17 torsion adjust,54.924955255002075,0.08049640922060164,20.210192340460285,0.07709852892567075,-6.929681,-41.644444,0.11146234817153751,-10.3239 +15 docked,49.591705359015535,0.08339231517341934,17.419734637085885,0.07694572781223565,-7.0023036,-39.174274,0.11346771901531096,-10.0438 +11 docked,50.084230264205374,0.0850375479104373,22.59411909000687,0.07605225628418619,-6.967471,-34.457584,0.11408475025407848,-10.9787 diff --git a/summaries/2026_jun_08_abfe/water_set/hsp90_kung/README.md b/summaries/2026_jun_08_abfe/water_set/hsp90_kung/README.md new file mode 100644 index 0000000..5da876e --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/hsp90_kung/README.md @@ -0,0 +1,33 @@ +# Hsp90 Kung + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 20.31 +- RMSE: 20.55 +- R²: 0.29 +- Kendall 𝜏: 0.04 +- Spearman ρ: 0.05 + +## System Details +- Ligands: 11 +- Host Atoms: 3924 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 4.10 Hours +- Average Time Per Molecule: 0.37 Hours +- Total Nanoseconds Simulated: 1750.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/hsp90_kung/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/hsp90_kung/dg_plot.png new file mode 100644 index 0000000..c118a7d Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/hsp90_kung/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/hsp90_kung/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/hsp90_kung/dg_results.csv new file mode 100644 index 0000000..93c56e1 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/hsp90_kung/dg_results.csv @@ -0,0 +1,12 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 16,27.698170267807512,0.07451978795754699,3.9637933208214466,0.06886203382231318,-7.4869604,-31.221334,0.10146515904182661,-10.33 +cmpd 9,22.626442071898364,0.07806290431600199,2.935166525269304,0.0674971454416055,-7.476019,-27.167295,0.10319729489194243,-7.920000000000001 +cmpd 13,27.614820097793274,0.07431990140938415,5.189681153272937,0.06920566124687522,-7.488609,-29.913748,0.10155230816735691,-10.15 +cmpd 14,26.907516277232624,0.06981633479912487,1.6351013603695528,0.07018754815345084,-7.609152,-32.88157,0.09899804301387213,-7.820000000000001 +cmpd 15,24.03104770661129,0.0753663137811573,1.0648060328577993,0.0680592993924545,-7.6273756,-30.593616,0.10154875423535051,-9.61 +cmpd 7,23.997120389207392,0.07149800110011847,4.809476212073783,0.06560754050501513,-7.61016,-26.797804,0.09703769129791653,-9.41 +cmpd 17,25.468466220115932,0.0768647934222447,3.2427603488978565,0.06921640281564209,-7.793928,-30.019634,0.10343648721114604,-10.74 +cmpd 11,24.653739271460132,0.07510387290700254,1.8193971688512562,0.06777602542822946,-7.4646764,-30.299019,0.1011641307404912,-9.19 +cmpd 12,27.77737566058259,0.0737503478250126,2.18462908297794,0.06704354009339313,-7.606697,-33.199444,0.09966920323030956,-9.19 +cmpd 10,30.072844435116767,0.07510158728786394,5.820164048020381,0.06961456850321317,-7.6224937,-31.875175,0.10240330346744292,-9.19 +cmpd 8,15.595425919478494,0.0719912213381818,3.3379827045998267,0.06600060013497039,-7.5953684,-19.852812,0.09766685808368843,-6.86 diff --git a/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/README.md b/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/README.md new file mode 100644 index 0000000..b092316 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/README.md @@ -0,0 +1,33 @@ +# Hsp90 Woodhead + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 21.85 +- RMSE: 21.88 +- R²: 0.92 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 4 +- Host Atoms: 4042 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.57 Hours +- Average Time Per Molecule: 0.39 Hours +- Total Nanoseconds Simulated: 677.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/dg_plot.png new file mode 100644 index 0000000..74d240f Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/dg_results.csv new file mode 100644 index 0000000..3e6ea31 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/hsp90_woodhead/dg_results.csv @@ -0,0 +1,5 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +4,31.25488499898742,0.0760414859968241,7.55674404187049,0.07283011004842116,-7.686887,-31.385027,0.10529260430946864,-8.93 +1,35.119827072852196,0.07474980711969115,6.915594248690089,0.07178121838200656,-7.768508,-35.97274,0.10363434265163428,-12.72 +3,25.19488819489344,0.07799435622777205,5.028202115880067,0.07047952081776769,-7.7818465,-27.948532,0.10512127500219332,-8.08 +2,27.542567540665807,0.07528488936799906,2.647425011648626,0.073603021820176,-7.660119,-32.55526,0.10528636848240688,-10.74 diff --git a/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/README.md b/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/README.md new file mode 100644 index 0000000..d516de6 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/README.md @@ -0,0 +1,33 @@ +# Scyt Dehyd + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 31.89 +- RMSE: 31.94 +- R²: 0.62 +- Kendall 𝜏: 0.52 +- Spearman ρ: 0.68 + +## System Details +- Ligands: 7 +- Host Atoms: 3060 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 2.60 Hours +- Average Time Per Molecule: 0.37 Hours +- Total Nanoseconds Simulated: 1145.60 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/dg_plot.png new file mode 100644 index 0000000..478d56d Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/dg_results.csv new file mode 100644 index 0000000..996b2b3 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/scyt_dehyd/dg_results.csv @@ -0,0 +1,8 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +3d,37.33979928831489,0.07073620199862943,1.675170167825794,0.07295819164341791,-7.327619,-42.99225,0.1016194272817388,-9.19327 +8d,40.25884623756372,0.07277780259754425,3.097206302351998,0.07252055165929848,-7.1608195,-44.322456,0.10274161262067137,-10.6284 +2d,38.86569266989475,0.0709956426125409,2.3795881661135865,0.07510666907859755,-7.281673,-43.76778,0.10335082491228406,-13.4817 +4d,39.33189558709555,0.07659984360365485,1.950583785746768,0.07352837269161375,-7.444918,-44.82623,0.10617889446957542,-15.343400000000003 +5d,40.580579910290915,0.0718575702594171,2.467004480504997,0.07397596093314693,-7.1930547,-45.30663,0.10313075777656995,-13.2535 +6d,38.018327039819425,0.0707333766342507,1.8649816426211898,0.07208394701382158,-7.2528005,-43.406147,0.10099161344970282,-9.40585 +7d,40.42531785329681,0.07832895260237978,2.6872470008402045,0.07376604277392167,-7.424852,-45.16292,0.10759578933355106,-15.2515 diff --git a/summaries/2026_jun_08_abfe/water_set/taf12/README.md b/summaries/2026_jun_08_abfe/water_set/taf12/README.md new file mode 100644 index 0000000..bb83aac --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/taf12/README.md @@ -0,0 +1,33 @@ +# Taf12 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 23.22 +- RMSE: 23.31 +- R²: 0.05 +- Kendall 𝜏: 0.21 +- Spearman ρ: 0.29 + +## System Details +- Ligands: 8 +- Host Atoms: 2702 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 3.16 Hours +- Average Time Per Molecule: 0.39 Hours +- Total Nanoseconds Simulated: 1372.80 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/taf12/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/taf12/dg_plot.png new file mode 100644 index 0000000..c22f350 Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/taf12/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/taf12/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/taf12/dg_results.csv new file mode 100644 index 0000000..e0f9d50 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/taf12/dg_results.csv @@ -0,0 +1,9 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 5 (1-Butenyl),36.12751707106504,0.0753919307281932,9.68478881055917,0.07295487099680352,-7.7944183,-34.23715,0.10491118348910629,-10.0 +cmpd 2 (methyl),35.55539896096011,0.0752075254086536,11.824027435588333,0.0694448956526497,-7.476892,-31.208263,0.10236584103254699,-9.86 +cmpd 3 (Allyl),32.54090342557353,0.07543082668808704,9.971611558606678,0.0711472806343774,-7.4710293,-30.040321,0.10369062231713665,-8.34 +cmpd 9 (methoxyethyl),36.71608186061489,0.07753476535534334,11.00639684500345,0.07344516688203272,-7.768605,-33.47829,0.10679809163574874,-7.690000000000001 +cmpd 6 (ethyl),33.957918408042126,0.0757133327312336,10.572262333363268,0.0712400824692145,-7.565024,-30.950678,0.10395988699248847,-8.53 +cmpd 8 (n-Butyl),29.58567001054826,0.07962715792373236,8.967502559995868,0.07434495586166082,-7.917284,-28.535448,0.10893877519544319,-8.28 +cmpd 7 (n-propyl),34.398787840308195,0.07679579567166456,9.67506030314742,0.07197732918134597,-7.171435,-31.89516,0.10525364672506075,-8.12 +cmpd 4 (Crotyl),36.31896330710773,0.07596105453292541,9.289711394823897,0.07350363378832103,-7.9181757,-34.94743,0.1057017785367951,-8.71 diff --git a/summaries/2026_jun_08_abfe/water_set/thrombin/README.md b/summaries/2026_jun_08_abfe/water_set/thrombin/README.md new file mode 100644 index 0000000..3999e2b --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/thrombin/README.md @@ -0,0 +1,33 @@ +# Thrombin + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 27.32 +- RMSE: 27.42 +- R²: 0.06 +- Kendall 𝜏: 0.26 +- Spearman ρ: 0.34 + +## System Details +- Ligands: 21 +- Host Atoms: 5256 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 9.32 Hours +- Average Time Per Molecule: 0.44 Hours +- Total Nanoseconds Simulated: 3858.00 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/thrombin/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/thrombin/dg_plot.png new file mode 100644 index 0000000..3f42664 Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/thrombin/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/thrombin/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/thrombin/dg_results.csv new file mode 100644 index 0000000..b693738 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/thrombin/dg_results.csv @@ -0,0 +1,22 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2d pose 2,47.58846637807755,0.08347382280524786,22.205709316458517,0.07761182161072654,-7.264537,-32.647293,0.11398014716369319,-6.63087 +2c pose 2,52.03470584716526,0.08413568447428924,24.18991247171213,0.07809822234885555,-7.420035,-35.264828,0.11479610505591396,-7.28564 +7b,44.097178305725414,0.08154983172364884,18.155833209507772,0.07707889233989534,-7.276318,-33.217667,0.11221198999438793,-7.4093 +7c pose 1,43.4027191202586,0.08409858407447215,17.812882752693863,0.07686349993876081,-7.210666,-32.800503,0.11393230211913978,-8.00849 +7f,47.64081804218646,0.08812935578566665,22.47696373969812,0.07677512267048253,-7.2816105,-32.445465,0.11688114823299889,-6.12277 +2b pose 1,43.912717079641915,0.08443055459206503,16.385195429983842,0.07768572155625304,-7.4672112,-34.994736,0.11473268881377859,-7.28564 +1a pose 2,44.550964358585304,0.08157612478469548,18.630295419559214,0.07789686964043868,-7.309887,-33.230553,0.11279444327921348,-7.4093 +7e pose 1,52.55362424119752,0.08461937612640007,20.078059177439588,0.07934277835242999,-7.2123814,-39.68795,0.11599877280688792,-5.65473 +6a pose 1,45.81817439241939,0.08338743980330533,17.409091651721997,0.07836691690512598,-7.0743237,-35.48341,0.11443268231656895,-9.91084 +5,41.997975671190936,0.08440806295274776,18.063429652014314,0.07709961505437854,-7.4154572,-31.350002,0.11432004081948355,-6.79363 +1c pose 2,45.339819267928384,0.08273869187956161,17.47415597494323,0.07805262115721645,-7.303562,-35.169224,0.11374490231853464,-8.57962 +2a pose 2,46.76345222872722,0.08308389743391811,17.892661982934918,0.07886532947356434,-7.3695717,-36.24036,0.11455424132603595,-6.61648 +7a pose 2,44.81283961251004,0.08260898437155051,15.79680506002144,0.07710533917631482,-7.1465383,-36.16257,0.11300211338020906,-7.62466 +3b pose 1,40.38667550017554,0.08757880770926592,15.275455518382492,0.08017395085536337,-7.1744347,-32.285652,0.11873461986941633,-7.25489 +6d pose 2,55.50779393422255,0.08731963225176324,23.420859756113774,0.07901498271545494,-7.442577,-39.529514,0.11776283654067958,-8.73291 +6c pose 1,44.114121104788126,0.08766601478986209,16.991317900847246,0.07854035511731844,-7.3602057,-34.48301,0.11770266577733407,-9.01441 +3a xtal pose,,,16.703298003224383,0.07662794583038644,,,,-8.12044 +1b pose 2,46.795218749088995,0.08163201882355316,18.61283896670203,0.07797685728789061,-7.382266,-35.564648,0.11289010926429736,-9.25606 +6b pose 2,47.17180519000036,0.0850635552096818,16.67605018461603,0.07920223961815712,-7.484439,-37.980198,0.11622737709095288,-9.0369 +6e pose 1,,,17.69885010382484,0.07598255292932324,,,,-8.64716 +1d pose 2,47.876706055638664,0.08299789844533303,17.467102699993237,0.07821567230004677,-7.422351,-37.83195,0.11404535299471924,-8.60129 diff --git a/summaries/2026_jun_08_abfe/water_set/urokinase/README.md b/summaries/2026_jun_08_abfe/water_set/urokinase/README.md new file mode 100644 index 0000000..7238f64 --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/urokinase/README.md @@ -0,0 +1,33 @@ +# Urokinase + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 37.11 +- RMSE: 37.14 +- R²: 0.02 +- Kendall 𝜏: 0.00 +- Spearman ρ: 0.00 + +## System Details +- Ligands: 4 +- Host Atoms: 4581 + +## Simulation Details +- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907) +- GPU: RTX 4090 +- MPS Processes: 2 +- Batch Mode: True +- Total Wallclock Time: 1.71 Hours +- Average Time Per Molecule: 0.43 Hours +- Total Nanoseconds Simulated: 726.40 +- 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 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/2026_jun_08_abfe/water_set/urokinase/dg_plot.png b/summaries/2026_jun_08_abfe/water_set/urokinase/dg_plot.png new file mode 100644 index 0000000..1b054ea Binary files /dev/null and b/summaries/2026_jun_08_abfe/water_set/urokinase/dg_plot.png differ diff --git a/summaries/2026_jun_08_abfe/water_set/urokinase/dg_results.csv b/summaries/2026_jun_08_abfe/water_set/urokinase/dg_results.csv new file mode 100644 index 0000000..57443ef --- /dev/null +++ b/summaries/2026_jun_08_abfe/water_set/urokinase/dg_results.csv @@ -0,0 +1,5 @@ +mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +"10302 (1GJ7, no water pose)",68.45965634485268,0.08063511977525462,29.82358323996944,0.07473478315010339,-7.4638233,-46.0999,0.10994230465868285,-10.8224 +11417 (no water pose),69.55366711825395,0.07906046318761852,28.05763872275613,0.073561505143405,-7.6680493,-49.16408,0.1079900545346838,-10.5656 +7806 (no water pose),71.93788789461625,0.08107008475318568,32.30702946484306,0.07255104020596703,-7.4550195,-47.08588,0.10879343765529498,-8.6515 +8696 (no water pose),70.00633518400912,0.07884256056938793,31.422412152736708,0.07358647099334893,-7.3637533,-45.94767,0.10784766140437439,-9.80217