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+2379,101 @@ ], [ 16, - 16 + 10 ], [ - 13, - 13 + 14, + 8 ], [ - 42, - 42 + 38, + 39 ], [ - 41, - 34 + 32, + 37 ], [ - 40, - 41 + 33, + 36 ], [ 39, - 38 - ], - [ - 38, - 40 + 30 ], [ - 37, - 39 + 40, + 29 ], [ - 36, - 43 + 41, + 28 ], [ - 35, - 36 + 34, + 27 ], [ - 34, - 37 + 37, + 26 ], [ - 33, - 23 + 36, + 25 ], [ - 32, - 35 + 35, + 24 ], [ - 31, - 33 + 42, + 23 ], [ 30, - 25 + 22 ], [ 29, - 26 + 21 ], [ 28, - 27 + 20 ], [ 27, - 28 + 19 ], [ 26, - 29 + 18 ], [ 25, - 30 + 17 ], [ 24, - 31 + 16 ], [ 23, - 32 - ], - [ - 19, - 19 - ], - [ - 18, - 18 + 15 ] ] }, { - "mol_a": "Example 22", - "mol_b": "Example 26", + "mol_a": "Example 1", + "mol_b": "Example 4", "core": [ [ 22, - 21 + 14 ], [ 21, - 22 + 13 ], [ 5, @@ -2945,47 +2497,39 @@ ], [ 20, - 20 + 12 ], [ 17, - 17 + 11 ], [ 15, - 15 + 9 ], [ - 14, - 14 + 13, + 7 ], [ 12, - 12 + 6 ], [ 11, - 11 + 32 ], [ 10, - 10 + 33 ], [ 9, - 9 - ], - [ - 8, - 8 - ], - [ - 7, - 7 + 34 ], [ 6, - 6 + 31 ], [ 0, @@ -2993,121 +2537,109 @@ ], [ 16, - 16 + 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24 ], [ 23, - 29 + 23 ], [ 19, @@ -3612,36 +3144,36 @@ ] }, { - "mol_a": "Example 24", - "mol_b": "Example 25", + "mol_a": "Example 22", + "mol_b": "Example 26", "core": [ - [ - 21, - 22 - ], [ 22, 21 ], [ - 1, - 5 + 21, + 22 ], [ - 2, - 4 + 5, + 1 + ], + [ + 4, + 2 ], [ 3, 3 ], [ - 4, - 2 + 2, + 4 ], [ - 5, - 1 + 1, + 5 ], [ 20, @@ -3691,10 +3223,6 @@ 0, 0 ], - [ - 33, - 23 - ], [ 16, 16 @@ -3704,27 +3232,35 @@ 13 ], [ - 36, - 43 + 42, + 42 ], [ - 45, - 42 + 41, + 35 ], [ 40, 41 ], + [ + 39, + 44 + ], [ 38, - 40 + 46 ], [ 37, - 39 + 45 ], [ - 39, + 36, + 43 + ], + [ + 35, 38 ], [ @@ -3732,56 +3268,48 @@ 37 ], [ - 35, - 36 + 33, + 23 ], [ 32, - 35 - ], - [ - 41, - 34 + 36 ], [ 31, - 33 - ], - [ - 23, - 32 + 34 ], [ - 24, - 31 + 30, + 26 ], [ - 25, - 30 + 29, + 27 ], [ - 26, - 29 + 28, + 28 ], [ 27, - 28 + 29 ], [ - 28, - 27 + 26, + 30 ], [ - 29, - 26 + 25, + 31 ], [ - 30, - 25 + 24, + 32 ], [ - 43, - 24 + 23, + 33 ], [ 19, @@ -3794,27 +3322,23 @@ ] }, { - "mol_a": "Example 26", - "mol_b": "Example 24", + "mol_a": "Example 22", + "mol_b": "Example 6", "core": [ [ - 23, - 33 - ], - [ - 21, + 22, 22 ], [ - 22, + 21, 21 ], [ - 1, + 5, 5 ], [ - 2, + 4, 4 ], [ @@ -3822,11 +3346,11 @@ 3 ], [ - 4, + 2, 2 ], [ - 5, + 1, 1 ], [ @@ -3887,62 +3411,50 @@ ], [ 42, - 45 - ], - [ - 24, - 43 - ], - [ - 25, 42 ], [ - 35, - 41 - ], - [ - 41, + 40, 40 ], [ - 44, + 39, 39 ], [ - 46, + 38, 38 ], [ - 45, + 37, 37 ], [ - 43, + 36, 36 ], [ - 38, + 35, 35 ], [ - 37, + 34, 34 ], [ - 36, - 32 + 32, + 33 ], [ - 34, + 31, 31 ], [ - 26, + 30, 30 ], [ - 27, + 29, 29 ], [ @@ -3950,23 +3462,23 @@ 28 ], [ - 29, + 27, 27 ], [ - 30, + 26, 26 ], [ - 31, + 25, 25 ], [ - 32, + 24, 24 ], [ - 33, + 23, 23 ], [ @@ -3980,8 +3492,8 @@ ] }, { - "mol_a": "Example 26", - "mol_b": "Example 25", + "mol_a": "Example 24", + "mol_b": "Example 23", "core": [ [ 22, @@ -4059,10 +3571,6 @@ 0, 0 ], - [ - 23, - 23 - ], [ 16, 16 @@ -4072,11 +3580,7 @@ 13 ], [ - 43, - 43 - ], - [ - 42, + 45, 42 ], [ @@ -4084,15 +3588,15 @@ 41 ], [ - 46, + 40, 40 ], [ - 45, + 39, 39 ], [ - 44, + 38, 38 ], [ @@ -4100,11 +3604,11 @@ 37 ], [ - 38, + 36, 36 ], [ - 36, + 34, 35 ], [ @@ -4112,45 +3616,49 @@ 34 ], [ - 34, + 33, 33 ], [ - 33, + 32, 32 ], [ - 32, + 31, 31 ], [ - 31, + 30, 30 ], [ - 30, + 29, 29 ], [ - 29, + 28, 28 ], [ - 28, + 27, 27 ], [ - 27, + 26, 26 ], [ - 26, + 25, 25 ], [ 24, 24 ], + [ + 23, + 23 + ], [ 19, 19 @@ -4162,23 +3670,23 @@ ] }, { - "mol_a": "Example 28", - "mol_b": "Example 23", + "mol_a": "Example 24", + "mol_b": "Example 25", "core": [ [ - 20, + 21, 22 ], [ - 19, + 22, 21 ], [ - 5, + 1, 5 ], [ - 4, + 2, 4 ], [ @@ -4186,15 +3694,15 @@ 3 ], [ - 2, + 4, 2 ], [ - 1, + 5, 1 ], [ - 18, + 20, 20 ], [ @@ -4214,11 +3722,11 @@ 12 ], [ - 7, + 11, 11 ], [ - 8, + 10, 10 ], [ @@ -4226,11 +3734,11 @@ 9 ], [ - 10, + 8, 8 ], [ - 11, + 7, 7 ], [ @@ -4241,6 +3749,10 @@ 0, 0 ], + [ + 33, + 23 + ], [ 16, 16 @@ -4250,43 +3762,47 @@ 13 ], [ - 46, + 36, + 43 + ], + [ + 45, 42 ], [ - 21, + 40, 41 ], [ - 39, + 38, 40 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"Example 2", - "mol_b": "Example 4", + "mol_a": "Example 26", + "mol_b": "Example 25", "core": [ - [ - 18, - 38 - ], [ 22, - 14 + 22 ], [ 21, - 13 + 21 ], [ 5, @@ -4728,35 +4236,47 @@ 1 ], [ - 8, - 34 + 20, + 20 ], [ - 11, - 32 + 17, + 17 ], [ - 6, - 31 + 15, + 15 ], [ - 20, + 14, + 14 + ], + [ + 12, 12 ], [ - 17, + 11, 11 ], [ - 15, + 10, + 10 + ], + [ + 9, 9 ], [ - 13, + 8, + 8 + ], + [ + 7, 7 ], [ - 12, + 6, 6 ], [ @@ -4764,121 +4284,141 @@ 0 ], [ - 7, - 35 + 23, + 23 ], [ 16, - 10 + 16 ], [ - 14, - 8 + 13, + 13 ], [ - 45, - 42 + 43, + 43 ], [ 42, + 42 + ], + [ + 41, 41 ], [ - 44, + 46, 40 ], [ - 43, + 45, 39 ], [ - 33, - 36 + 44, + 38 ], [ - 41, - 30 + 37, + 37 ], [ - 40, - 29 + 38, + 36 ], [ - 39, - 28 + 36, + 35 ], [ - 38, - 27 + 35, + 34 ], [ - 37, - 26 + 34, + 33 ], [ - 36, - 25 + 33, + 32 ], [ - 35, - 24 + 32, + 31 ], [ - 34, - 23 + 31, + 30 ], [ 30, - 22 + 29 ], [ 29, - 21 + 28 ], [ 28, - 20 + 27 ], [ 27, - 19 + 26 ], [ 26, - 18 + 25 ], [ - 25, - 17 + 24, + 24 ], [ - 24, - 16 + 19, + 19 ], [ - 23, - 15 + 18, + 18 ] ] }, { - "mol_a": "Example 2", - "mol_b": "Example 6", + "mol_a": "Example 29", + "mol_b": "Example 28", "core": [ [ - 22, - 22 + 20, + 20 ], [ - 21, - 21 + 19, + 19 ], [ - 1, + 11, + 11 + ], + [ + 10, + 10 + ], + [ + 9, + 9 + ], + [ + 8, + 8 + ], + [ + 5, 5 ], [ - 2, + 4, 4 ], [ @@ -4886,16 +4426,16 @@ 3 ], [ - 4, + 2, 2 ], [ - 5, + 1, 1 ], [ - 20, - 20 + 18, + 18 ], [ 17, @@ -4906,29 +4446,13 @@ 15 ], [ - 13, - 13 + 14, + 14 ], [ 12, 12 ], - [ - 11, - 11 - ], - [ - 10, - 10 - ], - [ - 9, - 9 - ], - [ - 8, - 8 - ], [ 7, 7 @@ -4941,115 +4465,107 @@ 0, 0 ], - [ - 32, - 32 - ], [ 16, 16 ], [ - 14, - 14 + 13, + 13 ], [ - 40, - 43 + 46, + 46 ], [ 45, 42 ], [ - 38, + 44, + 41 + ], + [ + 43, 40 ], [ - 36, + 42, 39 ], [ - 35, + 41, 38 ], [ - 37, + 40, 37 ], [ - 34, + 39, 36 ], [ - 41, + 38, 35 ], [ - 39, + 36, 34 ], [ - 33, + 34, 33 ], [ - 31, + 32, + 32 + ], + [ + 28, 31 ], [ - 24, + 27, 30 ], [ - 23, + 26, 29 ], [ - 26, + 25, 28 ], [ - 25, + 24, 27 ], 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28 ], [ 25, - 17 + 27 ], [ 24, - 16 + 26 ], [ 23, - 15 + 25 + ], + [ + 22, + 24 + ], + [ + 21, + 23 ] ] }, { - "mol_a": "Example 30", - "mol_b": "Example 5", + "mol_a": "Example 2", + "mol_b": "Example 1", "core": [ [ 22, - 21 + 22 ], [ 21, - 22 + 21 ], [ - 5, - 1 + 1, + 5 ], [ - 4, - 2 + 2, + 4 ], [ 3, 3 ], [ - 2, - 4 + 4, + 2 ], [ - 1, - 5 + 5, + 1 ], [ 20, @@ -5241,6 +4765,10 @@ 15, 15 ], + [ + 13, + 13 + ], [ 12, 12 @@ -5282,39 +4810,39 @@ 14 ], [ - 13, - 13 + 34, + 42 ], [ - 41, - 44 + 39, + 41 ], [ 40, - 43 - ], - [ - 39, 40 ], [ - 38, - 42 + 41, + 39 ], [ - 37, - 41 + 45, + 38 ], [ 36, - 45 + 37 ], [ 35, + 36 + ], + [ + 37, 35 ], [ - 34, + 38, 34 ], [ @@ -5330,36 +4858,36 @@ 31 ], [ - 30, - 23 + 24, + 30 ], [ - 29, - 24 + 23, + 29 ], [ - 28, - 25 + 26, + 28 ], [ - 27, - 26 + 25, + 27 ], [ - 26, - 27 + 28, + 26 ], [ - 25, - 28 + 27, + 25 ], [ - 24, - 29 + 30, + 24 ], [ - 23, - 30 + 29, + 23 ], [ 19, @@ -5372,16 +4900,16 @@ ] }, { - "mol_a": "Example 4", - "mol_b": "Example 3", + "mol_a": "Example 2", + "mol_b": "Example 30", "core": [ [ - 14, - 14 + 22, + 22 ], [ - 13, - 13 + 21, + 21 ], [ 1, @@ -5404,20 +4932,16 @@ 1 ], [ - 34, - 34 - ], - [ - 33, - 33 + 20, + 20 ], [ - 32, - 32 + 17, + 17 ], [ - 31, - 31 + 15, + 15 ], [ 12, @@ -5427,10 +4951,18 @@ 11, 11 ], + [ + 10, + 10 + ], [ 9, 9 ], + [ + 8, + 8 + ], [ 7, 7 @@ -5444,23 +4976,31 @@ 0 ], [ - 35, - 35 + 16, + 16 ], [ - 10, - 10 + 14, + 14 ], [ - 8, - 8 + 13, + 13 ], [ - 42, - 39 + 45, + 41 ], [ 38, + 40 + ], + [ + 36, + 39 + ], + [ + 35, 38 ], [ @@ -5468,82 +5008,86 @@ 37 ], [ - 36, + 34, 36 ], [ - 30, - 30 + 41, + 35 ], [ - 29, - 29 + 39, + 34 ], [ - 28, - 28 + 33, + 33 ], [ - 27, - 27 + 32, + 32 ], [ - 25, - 26 + 31, + 31 ], [ 24, - 25 - ], - [ - 26, - 24 + 30 ], [ 23, - 23 + 29 ], [ - 16, - 22 + 26, + 28 ], [ - 15, - 21 + 25, + 27 ], [ - 18, - 20 + 28, + 26 ], [ - 17, - 19 + 27, + 25 ], [ - 20, - 18 + 30, + 24 ], [ - 19, - 17 + 29, + 23 ], [ - 22, - 16 + 19, + 19 ], [ - 21, - 15 + 18, + 18 ] ] }, { - 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-7146,8 +6646,8 @@ ] }, { - "mol_a": "7b", - "mol_b": "7e pose 1", + "mol_a": "7c pose 1", + "mol_b": "6c pose 1", "core": [ [ 19, @@ -7183,11 +6683,11 @@ ], [ 25, - 21 + 25 ], [ 24, - 22 + 24 ], [ 23, @@ -7195,11 +6695,11 @@ ], [ 22, - 24 + 22 ], [ 21, - 25 + 21 ], [ 20, @@ -7299,7 +6799,7 @@ ], [ 38, - 38 + 36 ], [ 37, @@ -7307,7 +6807,7 @@ ], [ 36, - 36 + 38 ], [ 35, @@ -7331,23 +6831,19 @@ ], [ 30, - 26 + 30 ], [ 29, - 27 + 29 ], [ 28, 28 ], - [ - 27, - 29 - ], [ 26, - 30 + 26 ], [ 14, @@ -7360,8 +6856,8 @@ ] }, { - "mol_a": "7b", - "mol_b": "7f", + "mol_a": "7c pose 1", + "mol_b": "6e pose 1", "core": [ [ 19, @@ -7513,7 +7009,7 @@ ], [ 38, - 38 + 36 ], [ 37, @@ -7521,7 +7017,7 @@ ], [ 36, - 36 + 38 ], [ 35, @@ -7555,10 +7051,6 @@ 28, 28 ], - [ - 27, - 27 - ], [ 26, 26 @@ -7575,7 +7067,7 @@ }, { "mol_a": "7c pose 1", - "mol_b": "1a pose 2", + "mol_b": "7f", "core": [ [ 19, @@ -7727,7 +7219,7 @@ ], [ 38, - 36 + 38 ], [ 37, @@ -7735,7 +7227,7 @@ ], [ 36, - 38 + 36 ], [ 35, @@ 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[ 20, @@ -8105,14 +7593,6 @@ 2, 2 ], - [ - 54, - 52 - ], - [ - 55, - 57 - ], [ 51, 51 @@ -8166,16 +7646,16 @@ 39 ], [ - 38, - 36 + 36, + 38 ], [ 37, 37 ], [ - 36, - 38 + 38, + 36 ], [ 35, @@ -8198,20 +7678,20 @@ 31 ], [ - 30, - 26 + 27, + 29 ], [ 28, 28 ], [ - 27, - 29 + 29, + 27 ], [ - 26, - 30 + 30, + 26 ], [ 14, @@ -8411,14 +7891,6 @@ 30, 30 ], - [ - 29, - 29 - ], - [ - 28, - 28 - ], [ 27, 27 diff --git a/datasets/water_set/urokinase/urokinase_map.json b/datasets/water_set/urokinase/urokinase_map.json index 768ae49..6b1cff8 100644 --- a/datasets/water_set/urokinase/urokinase_map.json +++ b/datasets/water_set/urokinase/urokinase_map.json @@ -333,10 +333,6 @@ 26, 26 ], - [ - 25, - 25 - ], [ 18, 18 @@ -507,10 +503,6 @@ 26, 26 ], - [ - 25, - 25 - ], [ 18, 18 @@ -677,10 +669,6 @@ 26, 26 ], - [ - 25, - 25 - ], [ 18, 18 @@ -851,10 +839,6 @@ 26, 26 ], - [ - 25, - 25 - ], [ 18, 18 diff --git a/summaries/jan_14_2026/README.md b/summaries/jan_14_2026/README.md new file mode 100644 index 0000000..6680dd1 --- /dev/null +++ b/summaries/jan_14_2026/README.md @@ -0,0 +1,12 @@ +# Summary +- Number of Datasets: 53 +- Number of Ligands: 844 +- Number of Edges: 1424 +- Total Wallclock Time: 363.62 Hours +- Average Time Per Edge: 0.26 Hours +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) + +![Retrospective dG performance](dg_plot.png) + +## Notes: +- Enables the Heavy Matches Heavy atom parameter for the maps diff --git a/summaries/jan_14_2026/bayer_macrocycles/brd4/README.md b/summaries/jan_14_2026/bayer_macrocycles/brd4/README.md new file mode 100644 index 0000000..45f2b41 --- /dev/null +++ b/summaries/jan_14_2026/bayer_macrocycles/brd4/README.md @@ -0,0 +1,39 @@ +# Brd4 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.76 +- RMSE: 0.81 +- R²: 0.77 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 1776 +- Map Details: + - Edges: 3 + - Min Dummy Atoms: 8 + - Max Dummy Atoms: 47 + - Mean Dummy Atoms: 29.3 + - Median Dummy Atoms: 33.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.65 Hours +- Average Time Per Edge: 0.55 Hours +- Total Nanoseconds Simulated: 596.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/bayer_macrocycles/brd4/ddg_results.csv b/summaries/jan_14_2026/bayer_macrocycles/brd4/ddg_results.csv new file mode 100644 index 0000000..f7a9bef --- /dev/null +++ b/summaries/jan_14_2026/bayer_macrocycles/brd4/ddg_results.csv @@ -0,0 +1,4 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +25e,11,43.00883850456997,0.08529465358629584,41.817513045642876,0.08537082073363514,1.1913254589270945,0.12067872622438752,3.100000000000001 +61a,11,31.323177936636643,0.09407958245451799,27.108046684583723,0.09567271939207808,4.21513125205292,0.13417986835100026,3.8 +61a,25e,-21.11443281570642,0.06282074008016611,-23.450908965202565,0.06532678922636682,2.336476149496147,0.09063131233103681,0.6999999999999988 diff --git a/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_comparison_plot.png b/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_comparison_plot.png new file mode 100644 index 0000000..6bbe7a0 Binary files /dev/null and b/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_plot.png b/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_plot.png new file mode 100644 index 0000000..e2f86f9 Binary files /dev/null and b/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_plot.png differ diff --git a/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_results.csv b/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_results.csv new file mode 100644 index 0000000..baf67dd --- /dev/null +++ b/summaries/jan_14_2026/bayer_macrocycles/brd4/dg_results.csv @@ -0,0 +1,4 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +25e,CCOc1cc(=O)n(C)cc1-c1cc(NS(=O)(=O)CC)ccc1Oc1ccc(F)cc1F,-10.153953381843621,0.049196976859720465,-11.3 +11,COc1cc(=O)n(C)nc1-c1ccccc1Oc1ccccc1,-8.717178529153305,0.05511887239013786,-8.2 +61a,CCS(=O)(=O)Nc1ccc2c(c1)-c1cn(C)c(=O)cc1OCCCCc1cc(F)cc(F)c1O2,-12.628868089003074,0.045525698153451456,-12.0 diff --git a/summaries/jan_14_2026/bayer_macrocycles/ftase/README.md b/summaries/jan_14_2026/bayer_macrocycles/ftase/README.md new file mode 100644 index 0000000..d25aca9 --- /dev/null +++ b/summaries/jan_14_2026/bayer_macrocycles/ftase/README.md @@ -0,0 +1,39 @@ +# Ftase Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.13 +- RMSE: 1.43 +- R²: 0.28 +- Kendall 𝜏: 0.40 +- Spearman ρ: 0.50 + +## System Details +- Ligands: 5 +- Host Atoms: 11627 +- Map Details: + - Edges: 8 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 58 + - Mean Dummy Atoms: 36.6 + - Median Dummy Atoms: 39.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 5.85 Hours +- Average Time Per Edge: 0.73 Hours +- Total Nanoseconds Simulated: 1537.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/bayer_macrocycles/ftase/ddg_results.csv b/summaries/jan_14_2026/bayer_macrocycles/ftase/ddg_results.csv new file mode 100644 index 0000000..7bee2e7 --- /dev/null +++ b/summaries/jan_14_2026/bayer_macrocycles/ftase/ddg_results.csv @@ -0,0 +1,9 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +"lig 2, deprot",lig 49 stereo,14.242920038565162,0.09045952207335997,10.078837266104554,0.0901043008421326,4.164082772460609,0.12767815069145635,0.8100000000000003 +"lig 2, deprot",lig 51 stereo,24.167436929571597,0.09482742577235798,20.730371912640724,0.09132382102815319,3.4370650169308736,0.13165212100757898,1.0099999999999996 +"lig 2, deprot","lig 66, deprot",24.91227493331963,0.09282807568035889,20.593558050699098,0.09155269085135163,4.318716882620533,0.13038000934438376,0.11999999999999986 +lig 51 stereo,lig 49 stereo,-8.947602484332222,0.057223718205978505,-10.469576869689641,0.055974005193681384,1.5219743853574192,0.08004775563836569,-0.1999999999999992 +"lig 66, deprot",lig 49 stereo,-10.638641080644689,0.08409784182855433,-10.459712094831112,0.08318116161849273,-0.17892898581357589,0.11828589370006193,0.6900000000000004 +"lig 66, deprot","lig 68, deprot",7.4411601090516655,0.05181571714665017,8.599805789963472,0.05291564398214556,-1.1586456809118062,0.07406033973367143,0.18000000000000063 +"lig 68, deprot",lig 49 stereo,-16.248269796217144,0.08815676910435098,-18.594760047572645,0.0861285198065724,2.3464902513555033,0.12324665457118496,0.5099999999999998 +"lig 68, deprot",lig 51 stereo,-6.892183434085231,0.08944278876207255,-7.563005238802522,0.08871312376185514,0.670821804717291,0.12597631042828233,0.709999999999999 diff --git a/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_comparison_plot.png b/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_comparison_plot.png new file mode 100644 index 0000000..b08cdaa Binary files /dev/null and b/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_plot.png b/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_plot.png new file mode 100644 index 0000000..d81f08e Binary files /dev/null and b/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_plot.png differ diff --git a/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_results.csv b/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_results.csv new file mode 100644 index 0000000..5ea1046 --- /dev/null +++ b/summaries/jan_14_2026/bayer_macrocycles/ftase/dg_results.csv @@ -0,0 +1,6 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +"lig 2, deprot",N#Cc1ccc(Cn2cncc2CN2CCN(c3cccc(Cl)c3)C(=O)C2)cc1,-14.888979729781903,0.06247208734400297,-12.41 +lig 49 stereo,N#Cc1ccc2cc1Oc1ccc3cccc(c3c1)N1CC[C@H](NCc3cncn3C2)C1=O,-10.347635373686238,0.04278624128214929,-11.6 +lig 51 stereo,CN1Cc2cncn2Cc2ccc(C#N)c(c2)Oc2ccc3cccc(c3c2)N2CC[C@H]1C2=O,-11.694364845977955,0.041017331269102834,-11.4 +"lig 66, deprot",N#Cc1ccc2cc1Oc1ccc3cccc(c3c1)N1CC[C@H](NCCc3cncn3C2)C1=O,-10.725872862338361,0.044475073401399494,-12.29 +"lig 68, deprot",CN1CCc2cncn2Cc2ccc(C#N)c(c2)Oc2ccc3cccc(c3c2)N2CC[C@H]1C2=O,-12.153147188215547,0.04500686074378576,-12.11 diff --git a/summaries/jan_14_2026/dg_plot.png b/summaries/jan_14_2026/dg_plot.png new file mode 100644 index 0000000..873fd30 Binary files /dev/null and b/summaries/jan_14_2026/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/hsp90_2rings/README.md b/summaries/jan_14_2026/fragments/hsp90_2rings/README.md new file mode 100644 index 0000000..26fc545 --- /dev/null +++ b/summaries/jan_14_2026/fragments/hsp90_2rings/README.md @@ -0,0 +1,39 @@ +# Hsp90 2Rings Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.13 +- RMSE: 1.38 +- R²: 0.29 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.43 + +## System Details +- Ligands: 6 +- Host Atoms: 3282 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 6 + - Mean Dummy Atoms: 3.3 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.30 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 633.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/hsp90_2rings/ddg_results.csv b/summaries/jan_14_2026/fragments/hsp90_2rings/ddg_results.csv new file mode 100644 index 0000000..8a7ce80 --- /dev/null +++ b/summaries/jan_14_2026/fragments/hsp90_2rings/ddg_results.csv @@ -0,0 +1,10 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +17,19,-2.7314225927185025,0.039917425309484916,-0.6571712458965766,0.04054449593429901,-2.0742513468219252,0.056896897928663,-0.340000000000001 +18,15,3.413717655960131,0.04042746236089772,1.1008527999365616,0.039659291305667387,2.3128648560235696,0.05663249155572785,-0.92 +17,16,-2.358431079343603,0.03927323722820043,-4.445548228277871,0.04302577346293175,2.0871171489342677,0.05825465083979159,1.7999999999999996 +15,14,-3.7554189828934534,0.05246497887632149,-4.4529228708597115,0.05015605268971309,0.6975038879662584,0.07258239201008834,1.1599999999999997 +17,14,3.962648955359954,0.05362823278212844,4.317561020406376,0.05500476886679823,-0.35491206504642203,0.0768212988006845,1.1999999999999986 +14,16,-6.3839864000135496,0.05408480242987075,-8.981325260749719,0.05554984163041314,2.597338860736169,0.07753032154610306,0.600000000000001 +18,19,-8.060678548842187,0.03457257315882964,-8.524593290792211,0.03915037508207361,0.46391474195002336,0.05223039999741221,-1.2999999999999998 +18,16,-7.278851105004898,0.04365152310172677,-12.314640059590689,0.04658192273011175,5.035788954585791,0.06383831916909065,0.8400000000000006 +19,15,11.261219510980347,0.04635940321130491,9.684628272508851,0.046384621561946476,1.5765912384714955,0.06557993125608884,0.37999999999999984 diff --git a/summaries/jan_14_2026/fragments/hsp90_2rings/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/hsp90_2rings/dg_comparison_plot.png new file mode 100644 index 0000000..e395bf8 Binary files /dev/null and b/summaries/jan_14_2026/fragments/hsp90_2rings/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/hsp90_2rings/dg_plot.png b/summaries/jan_14_2026/fragments/hsp90_2rings/dg_plot.png new file mode 100644 index 0000000..75273b5 Binary files /dev/null and b/summaries/jan_14_2026/fragments/hsp90_2rings/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/hsp90_2rings/dg_results.csv b/summaries/jan_14_2026/fragments/hsp90_2rings/dg_results.csv new file mode 100644 index 0000000..faee522 --- /dev/null +++ b/summaries/jan_14_2026/fragments/hsp90_2rings/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1cccnc1)C2,-8.677918590860594,0.03198186811695411,-9.92 +19,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1-c1cccnc1)C2,-10.91755550863086,0.0307144743072796,-10.26 +18,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1-c1ccccc1)C2,-11.51434691548182,0.028746345551089427,-8.96 +15,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1ccccc1)C2,-9.35119994354701,0.031773512549098604,-9.88 +16,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccccc1-c1ccncc1)C2,-6.486818477552324,0.02893949647453926,-8.12 +14,Nc1ncc2c(n1)C[C@H](c1ccccc1-c1ccccc1)C/C2=N\O,-8.912160563927399,0.04074731301403412,-8.72 diff --git a/summaries/jan_14_2026/fragments/hsp90_single_ring/README.md b/summaries/jan_14_2026/fragments/hsp90_single_ring/README.md new file mode 100644 index 0000000..497eb04 --- /dev/null +++ b/summaries/jan_14_2026/fragments/hsp90_single_ring/README.md @@ -0,0 +1,39 @@ +# Hsp90 Single Ring Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.81 +- RMSE: 0.99 +- R²: 0.18 +- Kendall 𝜏: 0.39 +- Spearman ρ: 0.58 + +## System Details +- Ligands: 7 +- Host Atoms: 3282 +- Map Details: + - Edges: 11 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 5 + - Mean Dummy Atoms: 3.4 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.72 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 848.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/hsp90_single_ring/ddg_results.csv b/summaries/jan_14_2026/fragments/hsp90_single_ring/ddg_results.csv new file mode 100644 index 0000000..2243897 --- /dev/null +++ b/summaries/jan_14_2026/fragments/hsp90_single_ring/ddg_results.csv @@ -0,0 +1,12 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +10,3,2.461507129080574,0.03953976406472392,0.5145693720364851,0.0410686875007828,1.9469377570440887,0.05700903468162732,0.0 +10,12,9.400456370805202,0.04912993967947202,8.768305577495617,0.048133529208430656,0.6321507933095839,0.06877926727559262,-0.27999999999999853 +10,9,-1.6540753615273585,0.05161860056731718,-2.53624724073574,0.04945281795538327,0.8821718792083818,0.07148469156579271,0.9500000000000004 +11,12,3.3545294596762587,0.05070505864452189,4.620600542406523,0.05212752178390008,-1.266071082730264,0.07272057136378525,-0.4699999999999993 +11,2,-5.293935457600065,0.054705573649978585,-6.438739014448735,0.052668695955012675,1.1448035568486699,0.07593873400297636,1.1900000000000002 +3,12,7.339611311440828,0.053413824936491855,8.252961913896666,0.0547676247741716,-0.913350602455838,0.07650182623800986,-0.27999999999999853 +3,2,-2.002526138362708,0.04998773694499948,-2.627538335039489,0.04976641221864895,0.6250121966767814,0.0705370089385633,1.3800000000000008 +8,11,-1.9062198239131805,0.0397233873855086,-0.4634365594816763,0.04066815533163022,-1.4427832644315042,0.05684933036946686,-0.09000000000000116 +8,2,-6.939974510991315,0.047334119100704654,-6.750143353897588,0.04487186579094707,-0.1898311570937271,0.06522271974243683,1.099999999999999 +9,11,7.071455565949559,0.047058798242047256,6.834079646271781,0.04533389747454304,0.23737591967777757,0.0653428860107823,-0.7599999999999997 +9,8,10.343497271436599,0.052884821734818246,7.304172653739225,0.053549192241574735,3.039324617697375,0.07526167922421498,-0.6699999999999985 diff --git a/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_comparison_plot.png new file mode 100644 index 0000000..e98480d Binary files /dev/null and b/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_plot.png b/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_plot.png new file mode 100644 index 0000000..a4db73a Binary files /dev/null and b/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_results.csv b/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_results.csv new file mode 100644 index 0000000..d3bc13f --- /dev/null +++ b/summaries/jan_14_2026/fragments/hsp90_single_ring/dg_results.csv @@ -0,0 +1,8 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,Cc1nc(N)nc2c1C(=O)C[C@@H](c1ccc(F)cc1)C2,-9.547767440448201,0.03718091867452657,-8.31 +3,Cc1nc(N)nc2c1C(=O)C[C@@H](c1ccccc1)C2,-7.622915371921183,0.03375400186836495,-8.31 +12,Cc1nc(N)nc2c1/C(=N/O)C[C@@H](c1ccc(F)cc1)C2,-8.889668547797353,0.03229674986860941,-8.59 +9,Nc1ncc2c(n1)C[C@H](c1ccc(F)cc1)CC2=O,-8.658899546254009,0.039330189155972015,-7.36 +11,Nc1ncc2c(n1)C[C@H](c1ccc(F)cc1)C/C2=N\O,-7.913921013587744,0.03095995791486243,-8.12 +2,Nc1ncc2c(n1)C[C@H](c1ccccc1)CC2=O,-6.731272466383291,0.03705442471987773,-6.93 +8,Nc1ncc2c(n1)C[C@H](c1ccccc1)C/C2=N\O,-6.28555561360821,0.03517688944637703,-8.03 diff --git a/summaries/jan_14_2026/fragments/jak2_set1/README.md b/summaries/jan_14_2026/fragments/jak2_set1/README.md new file mode 100644 index 0000000..563e7d9 --- /dev/null +++ b/summaries/jan_14_2026/fragments/jak2_set1/README.md @@ -0,0 +1,39 @@ +# Jak2 Set1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.72 +- RMSE: 0.87 +- R²: 0.62 +- Kendall 𝜏: 0.42 +- Spearman ρ: 0.59 + +## System Details +- Ligands: 10 +- Host Atoms: 4824 +- Map Details: + - Edges: 17 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 7.0 + - Median Dummy Atoms: 8.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.80 Hours +- Average Time Per Edge: 0.22 Hours +- Total Nanoseconds Simulated: 1716.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/jak2_set1/ddg_results.csv b/summaries/jan_14_2026/fragments/jak2_set1/ddg_results.csv new file mode 100644 index 0000000..405f00b --- /dev/null +++ b/summaries/jan_14_2026/fragments/jak2_set1/ddg_results.csv @@ -0,0 +1,18 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +2_3E63,9,-0.3857705934064034,0.044421758987670056,-0.6981301176764507,0.04136872720604451,0.31235952427004726,0.06070143542130427,-0.4568700000000014 +2_3E63,8,3.023878299752616,0.044549791989075806,2.6443590001833712,0.041325409935907796,0.37951929956924463,0.060765726134398734,-0.8675500000000007 +4a,6,1.6789038404769314,0.05716593331736223,-1.920790841465091,0.05731504096099249,3.5996946819420224,0.08095034189183732,0.6655899999999993 +2_3E63,3,4.6904984134985055,0.056037753567058854,0.2759400033153291,0.05756933639859744,4.414558410183177,0.08033964350317527,2.6713899999999993 +10,1_3E62,-5.002215167465013,0.06006191462305544,-5.588193863409877,0.057463818193936124,0.5859786959448643,0.0831235465413558,1.1572900000000002 +1_3E62,7,-2.23943775453774,0.05929241429065104,-0.7560851600610138,0.05748408792159959,-1.4833525944767263,0.0825833564139433,-2.8738899999999994 +5,10,2.132892466890527,0.05008046925633249,0.07917573713379722,0.04973748692829302,2.0537167297567303,0.07058237036878673,0.6458199999999998 +4a,7,-10.69425791558599,0.0662647914024042,-10.560931862301654,0.06370795174233594,-0.1333260532843352,0.09192238951859305,-1.99635 +5,1_3E62,-4.840803926884386,0.05837654060106482,-5.93311400094557,0.05622091653306318,1.092310074061183,0.0810469737150341,1.80311 +5,3,17.143366954487263,0.06091713773970006,13.426707289143625,0.059484863222977885,3.7166596653436392,0.08514309498164827,2.55418 +6,1_3E62,-2.9629184764204832,0.05730022309722496,-2.1605274380274087,0.05584559322083013,-0.802391038393075,0.08001278553567662,0.21195000000000025 +8,5,-16.133168253476903,0.04743229646792425,-15.730141539681505,0.04702467849030253,-0.4030267137953975,0.06679178943056834,0.9847599999999999 +5,4a,1.0495058846563061,0.06964569214231822,1.9685265251254613,0.06817980964509011,-0.9190206404691553,0.09746285896290591,0.9255700000000003 +9,10,-10.918040674228056,0.0368464865471289,-12.476107016695419,0.03797297343261091,1.5580663424673638,0.05291134360589916,1.2199000000000002 +6,7,-11.405099006705678,0.0623358373414606,-8.546333029095194,0.06039191407285387,-2.858765977610482,0.0867925106356764,-2.6619399999999995 +8,3,0.7268739964213844,0.06466760495009907,-2.49920934434494,0.06230639351151739,3.2260833407663245,0.08979969823108615,3.5389399999999998 +9,8,3.390687730286243,0.05426662655057866,3.207620031439247,0.050034109397312856,0.18306769884699578,0.0738124573521451,-0.4106799999999993 diff --git a/summaries/jan_14_2026/fragments/jak2_set1/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/jak2_set1/dg_comparison_plot.png new file mode 100644 index 0000000..3176229 Binary files /dev/null and b/summaries/jan_14_2026/fragments/jak2_set1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/jak2_set1/dg_plot.png b/summaries/jan_14_2026/fragments/jak2_set1/dg_plot.png new file mode 100644 index 0000000..b0e6289 Binary files /dev/null and b/summaries/jan_14_2026/fragments/jak2_set1/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/jak2_set1/dg_results.csv b/summaries/jan_14_2026/fragments/jak2_set1/dg_results.csv new file mode 100644 index 0000000..75736e6 --- /dev/null +++ b/summaries/jan_14_2026/fragments/jak2_set1/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2_3E63,Nc1n[nH]c2ccc(-c3ccccc3)cc12,-8.43347478661352,0.04786984267088605,-7.90701 +9,Nc1n[nH]c2ccc(-c3cccc(Cl)c3)cc12,-8.107856708504924,0.04588738907365077,-8.36388 +8,Nc1n[nH]c2ccc(-c3ccccc3Cl)cc12,-7.875102801815562,0.040133397859299924,-8.77456 +4a,Nc1n[nH]c2ccc(-c3ccn[nH]3)cc12,-8.903247150340457,0.056587609048642504,-6.86423 +6,Cc1noc(C)c1-c1ccc2[nH]nc(N)c2c1,-5.585606583463489,0.051765724494611594,-6.19864 +3,Nc1n[nH]c2cc(-c3ccccc3)ccc12,-4.354776702783188,0.04747226977641517,-5.23562 +10,Nc1n[nH]c2ccc(-c3cccc(Cl)n3)cc12,-6.565247873206662,0.03782190695894077,-7.14398 +1_3E62,Nc1n[nH]c2ccc(Br)cc12,-6.620489912807984,0.04237495040644028,-5.98669 +7,Cc1nc(C)c(-c2ccc3[nH]nc(N)c3c2)s1,-8.495046251571203,0.055237849254670186,-8.86058 +5,Nc1n[nH]c2ccc(-c3ccncc3)cc12,-8.184141228893004,0.030188827628307602,-7.7898000000000005 diff --git a/summaries/jan_14_2026/fragments/jak2_set2/README.md b/summaries/jan_14_2026/fragments/jak2_set2/README.md new file mode 100644 index 0000000..acc58d7 --- /dev/null +++ b/summaries/jan_14_2026/fragments/jak2_set2/README.md @@ -0,0 +1,39 @@ +# Jak2 Set2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.39 +- RMSE: 2.02 +- R²: 0.40 +- Kendall 𝜏: 0.50 +- Spearman ρ: 0.67 + +## System Details +- Ligands: 8 +- Host Atoms: 4843 +- Map Details: + - Edges: 12 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 38 + - Mean Dummy Atoms: 19.1 + - Median Dummy Atoms: 21.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.81 Hours +- Average Time Per Edge: 0.32 Hours +- Total Nanoseconds Simulated: 1698.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/jak2_set2/ddg_results.csv b/summaries/jan_14_2026/fragments/jak2_set2/ddg_results.csv new file mode 100644 index 0000000..b41af34 --- /dev/null +++ b/summaries/jan_14_2026/fragments/jak2_set2/ddg_results.csv @@ -0,0 +1,13 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +13_3E64,21,-0.34380265706013735,0.04265730042064107,0.2377554328681883,0.04623745644128543,-0.5815580899283256,0.06290904273104617,1.3565999999999998 +18,12,-1.4049423909168084,0.07813936248962995,-6.9329625879257435,0.07454696235983496,5.528020197008936,0.10799541456638073,0.8903099999999998 +14,15,-8.731140455085832,0.07474978084473567,-8.332907010024721,0.07169271267557246,-0.3982334450611105,0.10357304083166718,0.4106800000000002 +14,12,-17.607781407946973,0.08190228357654634,-21.515348600521854,0.07605041838367345,3.907567192574882,0.11176605115769633,0.3549700000000001 +13_3E64,12,7.068105335646288,0.07760361026502104,0.1355874042634363,0.07847443894813498,6.9325179313828516,0.1103655648034741,2.2621099999999994 +13_3E64,15,9.105283111027491,0.08390808256534517,7.113244130028149,0.07806776378449275,1.9920389809993415,0.1146086474141639,2.3178199999999998 +18,15,2.66160689169106,0.08223850380479875,1.6114718358900346,0.07916203617605293,1.0501350558010254,0.11414814707033404,0.9460199999999999 +18,22-flip,-10.575724341822944,0.0643055744934775,-8.690276974403552,0.06354575097418975,-1.8854473674193921,0.09040613573098855,-1.78246 +20,22-flip,2.4502314783343575,0.054936618641522224,2.157077682154728,0.05555399500457902,0.29315379617962956,0.07812988179136608,-2.03993 +21,20,-1.248619791025257,0.03533134315526002,-0.7006369628613455,0.037109278526400336,-0.5479828281639115,0.05123868032946103,0.2726699999999999 +20,14,17.412511809722485,0.07143598718656692,13.295777608671374,0.06991640596715167,4.116734201051113,0.09995701120323133,0.27786999999999956 +21,22-flip,0.8713911423035506,0.05297389436351609,1.8239826115332751,0.0558112633664338,-0.9525914692297244,0.07694888304968693,-1.7672600000000003 diff --git a/summaries/jan_14_2026/fragments/jak2_set2/dg_plot.png b/summaries/jan_14_2026/fragments/jak2_set2/dg_plot.png new file mode 100644 index 0000000..4e96f33 Binary files /dev/null and b/summaries/jan_14_2026/fragments/jak2_set2/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/jak2_set2/dg_results.csv b/summaries/jan_14_2026/fragments/jak2_set2/dg_results.csv new file mode 100644 index 0000000..e656552 --- /dev/null +++ b/summaries/jan_14_2026/fragments/jak2_set2/dg_results.csv @@ -0,0 +1,9 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +13_3E64,CC(C)(C)NS(=O)(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-9.593338222476206,0.04520776544436388,-9.69694 +21,Cc1cc(-c2ccc(S(=O)(=O)NC(C)(C)C)cc2)cc2c(N)n[nH]c12,-10.135446730198213,0.04312164937891858,-8.34034 +18,CCS(=O)(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-8.633595313651353,0.058574357783017984,-8.32514 +12,CC(C)(C)NS(=O)(=O)c1cccc(-c2ccc3[nH]nc(N)c3c2)c1,-2.9083830514386246,0.05596869804624294,-7.43483 +14,CC(C)(C)NC(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-6.858633508405016,0.05066500022997353,-7.7898000000000005 +15,CC(C)(C)NC(=O)Nc1ccc(-c2ccc3[nH]nc(N)c3c2)cc1,-7.46526869496677,0.05875605523269489,-7.37912 +22-flip,CC(C)(C)NS(=O)(=O)c1ccc(-c2ccc3[nH]nc(N)c3c2)c(Cl)c1,-10.731370671413153,0.045064415685635094,-10.1076 +20,CC(C)(C)NS(=O)(=O)c1ccc(-c2cc(Cl)c3[nH]nc(N)c3c2)cc1,-10.815403807450664,0.04597359236148107,-8.06767 diff --git a/summaries/jan_14_2026/fragments/liga/README.md b/summaries/jan_14_2026/fragments/liga/README.md new file mode 100644 index 0000000..3dbab9c --- /dev/null +++ b/summaries/jan_14_2026/fragments/liga/README.md @@ -0,0 +1,39 @@ +# Liga Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.18 +- RMSE: 1.58 +- R²: 0.96 +- Kendall 𝜏: 0.82 +- Spearman ρ: 0.93 + +## System Details +- Ligands: 11 +- Host Atoms: 4930 +- Map Details: + - Edges: 18 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 20 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.39 Hours +- Average Time Per Edge: 0.24 Hours +- Total Nanoseconds Simulated: 1745.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/liga/ddg_results.csv b/summaries/jan_14_2026/fragments/liga/ddg_results.csv new file mode 100644 index 0000000..ea8711a --- /dev/null +++ b/summaries/jan_14_2026/fragments/liga/ddg_results.csv @@ -0,0 +1,19 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +10,3,0.028889043419257535,0.04262496448733679,-1.1114022898384213,0.04503920293748119,1.140291333257679,0.06201142958189511,0.5099999999999998 +12,11,12.848138432311192,0.05773703471509617,11.225059894390988,0.0564404117551781,1.6230785379202035,0.08074085246507041,-0.030000000000000387 +11,13,-49.372776200798796,0.06101850131678238,-44.638323620396335,0.06112383679910907,-4.734452580402467,0.08636770766895631,-1.5900000000000003 +12,13,-36.09681501298827,0.041930117310551025,-33.60549532368045,0.04238261407949757,-2.4913196893078253,0.059618962703893094,-1.6200000000000006 +10,8,53.53918189759092,0.0663423599175029,52.28735862832895,0.06499735287835605,1.2518232692619724,0.09287607119499099,0.7099999999999999 +3,4,-11.565361859789151,0.037854411851571214,-11.92153919109329,0.03722831307814927,0.3561773313041385,0.053093349783876656,-0.47000000000000014 +12,10,-11.7389770485322,0.07163731371647492,-16.703364010080215,0.0714167232938143,4.964386961548012,0.1011545999079522,2.5100000000000002 +10,13,-25.161189170710948,0.07335925928147599,-16.6367175526308,0.07539022108358598,-8.524471618080149,0.10519156980176117,-4.130000000000001 +3,7,-11.272327965126495,0.04266458682449242,-12.000269978051985,0.04366648970796775,0.7279420129254909,0.0610494004255628,0.7799999999999999 +5,10,7.325394808485862,0.04994677820461069,10.933972225016277,0.04965112328321835,-3.608577416530415,0.07042666182850016,-1.7399999999999995 +5,4,-4.275557880479611,0.04340385723962782,-1.7963182152515904,0.04270443259543169,-2.4792396652280204,0.06088976421842806,-1.7 +5,7,-3.8342710734174945,0.04296403218698556,-2.053053385085247,0.04462208928887668,-1.7812176883322477,0.0619438367738778,-0.4499999999999999 +6,4,1.9511491456693688,0.0480533651551301,2.1626140997992946,0.048896954102498884,-0.21146495412992586,0.0685568233163859,-1.2000000000000002 +7,4,-0.8358858206199955,0.03628587852183837,-0.035024175296515914,0.03640253267016499,-0.8008616453234796,0.05139853465716742,-1.25 +9,6,-17.688306094424572,0.046189657703536426,-18.777466417493997,0.046531054454004045,1.0891603230694273,0.06556388874503517,1.0800000000000003 +6,8,67.75487041718043,0.06456078450801035,68.92229351000015,0.06350589169240302,-1.1674230928197245,0.09055988723456414,-0.53 +9,11,28.486176976637317,0.06545498428546692,31.623804156262107,0.06447992502082142,-3.13762717962479,0.0918804424156821,-2.7 +9,8,50.309458968404215,0.06857028901216973,49.64847637457492,0.06568751403392661,0.6609825938292974,0.09495648495584592,0.5500000000000004 diff --git a/summaries/jan_14_2026/fragments/liga/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/liga/dg_comparison_plot.png new file mode 100644 index 0000000..cf86891 Binary files /dev/null and b/summaries/jan_14_2026/fragments/liga/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/liga/dg_plot.png b/summaries/jan_14_2026/fragments/liga/dg_plot.png new file mode 100644 index 0000000..ba795c0 Binary files /dev/null and b/summaries/jan_14_2026/fragments/liga/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/liga/dg_results.csv b/summaries/jan_14_2026/fragments/liga/dg_results.csv new file mode 100644 index 0000000..edcc221 --- /dev/null +++ b/summaries/jan_14_2026/fragments/liga/dg_results.csv @@ -0,0 +1,12 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,FC(F)(F)c1cccc(-c2nc[nH]n2)n1,-6.352347017709052,0.03297585522479158,-6.54 +3,Clc1cncc(-c2nc[nH]n2)n1,-5.263890573895786,0.03984646385400407,-6.03 +12,OCCNc1cc(-c2n[nH]c3cnccc23)nc(C(F)(F)F)c1,-11.507315701352223,0.05181232908986823,-9.05 +11,FC(F)(F)c1cccc(-c2n[nH]c3cnccc23)n1,-9.569456560439056,0.05385588515357027,-9.08 +13,OCCNc1cc(C(F)(F)F)nc(-c2n[nH]c3cnccc23)n1,-14.236467350725867,0.04921310535842416,-10.67 +8,c1cc(-c2nc[nH]n2)nc(C2CCC2)c1,-5.5139273334126555,0.048086689828737365,-5.83 +4,Clc1cccc(-c2nc[nH]n2)n1,-5.059467128109337,0.03299791286278627,-6.5 +7,Cc1cccc(-c2nc[nH]n2)n1,-4.385545377914826,0.04352418196780433,-5.25 +5,c1ccc(-c2nc[nH]n2)nc1,-2.6338562073479967,0.040797873315137664,-4.8 +6,COc1cccc(-c2nc[nH]n2)n1,-4.807202613717635,0.046061608307634054,-5.3 +9,CC(F)(F)c1cccc(-c2nc[nH]n2)n1,-6.1005241353755615,0.051859028825104084,-6.38 diff --git a/summaries/jan_14_2026/fragments/mcl1/README.md b/summaries/jan_14_2026/fragments/mcl1/README.md new file mode 100644 index 0000000..6c78dfb --- /dev/null +++ b/summaries/jan_14_2026/fragments/mcl1/README.md @@ -0,0 +1,39 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.56 +- RMSE: 0.70 +- R²: 0.37 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.40 + +## System Details +- Ligands: 12 +- Host Atoms: 2428 +- Map Details: + - Edges: 20 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 19 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.80 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 2010.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/mcl1/ddg_results.csv b/summaries/jan_14_2026/fragments/mcl1/ddg_results.csv new file mode 100644 index 0000000..d269034 --- /dev/null +++ b/summaries/jan_14_2026/fragments/mcl1/ddg_results.csv @@ -0,0 +1,21 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +2,3,0.2513256220882888,0.04337339661624909,2.307619373981208,0.04476044918502187,-2.056293751892919,0.06232775742215801,-1.0599999999999994 +2,13 flipped,9.216779333351441,0.053753771730871015,7.848273316564457,0.05456193989130389,1.3685060167869845,0.07659290606836149,0.11999999999999986 +10,15,5.1578163922382325,0.06470094625475757,4.741887625774669,0.06054243894776558,0.415928766463564,0.08860925098433545,-0.2700000000000001 +11,14,-0.321838924786116,0.06275047690524299,-1.290791360126712,0.06178192871195184,0.9689524353405959,0.08806037171852123,-0.060000000000000775 +2,4,-4.403535299926476,0.042571465664672854,-3.768165468004645,0.041322399492816846,-0.6353698319218316,0.05932849558755362,-0.4799999999999994 +2,14,8.044682552764492,0.06601348969340506,7.3948731629462925,0.06389179832429842,0.6498093898181997,0.09186916084635866,-0.28000000000000025 +2,15,20.618102130262326,0.07173343060760683,20.761811710236714,0.06997559376266901,-0.1437095799743883,0.10021112108530882,0.02000000000000026 +2,5,0.2910410919405741,0.04248454703700052,0.27966866432087095,0.04307070209017397,0.011372427619703123,0.06049811662754159,-0.7099999999999999 +3,4,-4.559935753153139,0.053614637702749816,-5.862590327209198,0.05448976950223679,1.3026545740560587,0.07644386408603385,0.5799999999999998 +3,11,7.7054196613428925,0.06171361695936215,6.222109279713129,0.061255482459906134,1.4833103816297637,0.08695288752883794,0.8399999999999999 +7,13 flipped,-4.443018115782945,0.049458762406023676,-5.840933471152679,0.047284397524342076,1.3979153553697345,0.06842502048209784,0.6699999999999994 +4,11,12.209430724165104,0.06115351443867345,12.311959902673328,0.06266953808897201,-0.1025291785082249,0.08756268230522724,0.25999999999999995 +5,10,15.38276410468534,0.06057693954053541,15.826644724064623,0.06084848091587595,-0.44388061937928425,0.08586095290565673,1.0000000000000002 +5,8,11.83269852353915,0.0588287683825918,13.16040897503346,0.05693322732195004,-1.3277104514943088,0.08186706518927786,-0.33 +7,14,-6.957813037163047,0.05505189868046767,-6.27591583908485,0.054295654116724594,-0.6818971980781972,0.0773222452098196,0.26999999999999924 +7,8,-1.6004351201194598,0.049037323915629635,-0.10355854175823109,0.04845175828608582,-1.4968765783612286,0.06893643461783955,-0.4900000000000004 +7,9,0.20981425993955882,0.05143297648821882,0.8364570160671513,0.053098541825128444,-0.6266427561275925,0.07392432762218797,0.39999999999999925 +8,10,3.4693824508379794,0.04952779843492179,2.640383808877657,0.04928728800692886,0.8289986419603227,0.0698730246725315,1.3300000000000003 +9,13 flipped,-4.23828322443242,0.04790597711555528,-6.735873223683552,0.049264435952168395,2.4975899992511317,0.06871657218663783,0.2700000000000001 +9,15,7.048839865349963,0.05849575931819921,6.227119262009276,0.05322953669576851,0.8217206033406881,0.07908942682216666,0.1700000000000005 diff --git a/summaries/jan_14_2026/fragments/mcl1/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/mcl1/dg_comparison_plot.png new file mode 100644 index 0000000..cbf04d8 Binary files /dev/null and b/summaries/jan_14_2026/fragments/mcl1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/mcl1/dg_plot.png b/summaries/jan_14_2026/fragments/mcl1/dg_plot.png new file mode 100644 index 0000000..d8621f8 Binary files /dev/null and b/summaries/jan_14_2026/fragments/mcl1/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/mcl1/dg_results.csv b/summaries/jan_14_2026/fragments/mcl1/dg_results.csv new file mode 100644 index 0000000..94dfbd1 --- /dev/null +++ b/summaries/jan_14_2026/fragments/mcl1/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2,O=C([O-])c1sc2ccccc2c1Cl,-5.372051376884223,0.02662813604997351,-5.33 +3,O=C([O-])c1sc2cccc(Cl)c2c1Cl,-7.4440543016477525,0.04346070201436606,-6.39 +13 flipped,Cn1c(C(=O)[O-])cc2ccccc21,-3.707620130691449,0.04318688694595006,-5.21 +10,Cc1ccc2c(C)c(C(=O)[O-])oc2c1C,-5.758398176540274,0.04894792633940242,-5.04 +15,Cc1cccc2c(-c3ccccc3)c(C(=O)[O-])[nH]c12,-5.326005602188086,0.04770916901242341,-5.31 +11,O=C([O-])c1cc2c(Br)cc(Cl)cc2o1,-6.113105345322451,0.05720124610343813,-5.55 +14,Cn1c(C(=O)[O-])cc2cc(Br)ccc21,-5.26330615236839,0.055924192524257524,-5.61 +4,O=C([O-])c1sc2cc(Cl)ccc2c1Cl,-6.0472718713528035,0.044735430349262674,-5.81 +5,Cc1ccc2c(Cl)c(C(=O)[O-])sc2c1,-5.323588766581493,0.046757643594504274,-6.04 +7,Cc1c(C(=O)[O-])oc2ccc(Cl)cc12,-5.0565565205482175,0.03340105935175616,-5.88 +8,Cc1c(C(=O)[O-])oc2cc(Cl)ccc12,-6.591626767026813,0.0477882929407905,-6.37 +9,Cc1c(C(=O)[O-])oc2c(C)cccc12,-6.016414988848037,0.04687438120267969,-5.48 diff --git a/summaries/jan_14_2026/fragments/mup1/README.md b/summaries/jan_14_2026/fragments/mup1/README.md new file mode 100644 index 0000000..6263a12 --- /dev/null +++ b/summaries/jan_14_2026/fragments/mup1/README.md @@ -0,0 +1,39 @@ +# Mup1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.40 +- RMSE: 0.49 +- R²: 0.98 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 6 +- Host Atoms: 2486 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 7.8 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.40 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 719.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/mup1/ddg_results.csv b/summaries/jan_14_2026/fragments/mup1/ddg_results.csv new file mode 100644 index 0000000..d97ab97 --- /dev/null +++ b/summaries/jan_14_2026/fragments/mup1/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +MT,ET,2.4710776114857547,0.03814111172428981,3.9299864538016767,0.03815485046930749,-1.458908842315922,0.05394939311892184,-1.32 +IPT,ET,-2.5286830907169833,0.042140234561513855,-3.8725662012331212,0.04462368771660539,1.3438831105161382,0.0613764847016227,0.8899999999999997 +IBT,PT,-2.602768060551617,0.042959217110735484,-3.7354545576064324,0.043488607593664276,1.1326864970548158,0.06112898923753789,0.8900000000000013 +MT,IPT,4.498019005716746,0.04237167181365782,7.7453607552144135,0.04468646624483828,-3.247341749497667,0.06158115651508501,-2.21 +IBT,ET,-4.024231007489239,0.0451905726096628,-6.89603502459881,0.04623815396868682,2.8718040171095702,0.06465411615064577,2.1300000000000003 +IBT,SBT_S,1.345949898575452,0.05372631816109064,1.3266656144844218,0.05348878756024861,0.019284284091030193,0.07581271435459981,0.6700000000000002 +MT,PT,3.048442161381274,0.04274081461955976,6.509131349355723,0.04341514205689374,-3.4606891879744492,0.060923327175752946,-2.559999999999999 +PT,SBT_S,4.231825996567645,0.04405869201133767,5.181317569662417,0.04340165159933939,-0.9494915730947717,0.06184554715822595,-0.22000000000000114 +PT,IPT,1.2059399656946816,0.05453190210947114,0.7020104965774302,0.052171834046822796,0.5039294691172514,0.0754693885988628,0.3499999999999994 +SBT_S,ET,-5.927397584869023,0.051038906218171136,-8.356495071058692,0.05085469135745328,2.429097486189669,0.07204977155417705,1.4600000000000002 diff --git a/summaries/jan_14_2026/fragments/mup1/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/mup1/dg_comparison_plot.png new file mode 100644 index 0000000..362b980 Binary files /dev/null and b/summaries/jan_14_2026/fragments/mup1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/mup1/dg_plot.png b/summaries/jan_14_2026/fragments/mup1/dg_plot.png new file mode 100644 index 0000000..60a0a42 Binary files /dev/null and b/summaries/jan_14_2026/fragments/mup1/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/mup1/dg_results.csv b/summaries/jan_14_2026/fragments/mup1/dg_results.csv new file mode 100644 index 0000000..5f786ee --- /dev/null +++ b/summaries/jan_14_2026/fragments/mup1/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +MT,CC1=NCCS1,-4.878565708347423,0.02611422466827822,-5.64 +ET,CCC1=NCCS1,-6.513012232872046,0.026687944479017678,-6.96 +IPT,CC(C)C1=NCCS1,-7.941401252385067,0.03565346355364662,-7.85 +IBT,CC(C)CC1=NCCS1,-9.353907537403735,0.032801751533768964,-9.09 +PT,CCCC1=NCCS1,-8.295986455467537,0.02513162095948001,-8.2 +SBT_S,CC[C@H](C)C1=NCCS1,-9.177126813524193,0.035049948604581646,-8.42 diff --git a/summaries/jan_14_2026/fragments/p38/README.md b/summaries/jan_14_2026/fragments/p38/README.md new file mode 100644 index 0000000..3d9447b --- /dev/null +++ b/summaries/jan_14_2026/fragments/p38/README.md @@ -0,0 +1,39 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.98 +- RMSE: 1.06 +- R²: 0.63 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.77 + +## System Details +- Ligands: 6 +- Host Atoms: 5667 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 4 + - Max Dummy Atoms: 32 + - Mean Dummy Atoms: 19.6 + - Median Dummy Atoms: 20.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.47 Hours +- Average Time Per Edge: 0.35 Hours +- Total Nanoseconds Simulated: 1325.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/p38/ddg_results.csv b/summaries/jan_14_2026/fragments/p38/ddg_results.csv new file mode 100644 index 0000000..02382d9 --- /dev/null +++ b/summaries/jan_14_2026/fragments/p38/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +1_1W7H,3,23.915817159905487,0.04607628702535669,23.88229741840056,0.047117825731386814,0.03351974150492674,0.0659023044187105,-0.14999999999999938 +4,3,25.939591019184192,0.05814681609330169,24.589285547808288,0.05938363498373552,1.3503054713759042,0.08311118050942236,1.3100000000000007 +1_1W7H,5_1WBW,7.758651804477968,0.06318526721886121,9.418659954037066,0.0614949769908751,-1.660008149559098,0.08817034755872949,-2.0000000000000004 +4,5_1WBW,10.657214439796205,0.06387804880223286,10.272317861406243,0.06295878893092892,0.3848965783899612,0.08968954355123956,-0.5400000000000001 +1_1W7H,6,1.4957302067498064,0.07118533795216135,5.251742391055578,0.07083930623489605,-3.7560121843057717,0.10042688707315787,-1.0999999999999999 +4,7,7.354201906724528,0.07103460847233292,9.546088933394778,0.06749139668222373,-2.19188702667025,0.09798471425143268,-0.8999999999999998 +5_1WBW,3,15.9812147755005,0.0691572026123798,14.188926021671117,0.069808184137772,1.7922887538293848,0.0982644454814804,1.850000000000001 +6,3,21.674386582506656,0.06420546220646481,18.35528690723102,0.06558281014834211,3.319099675275639,0.09177933516919409,0.9500000000000004 +6,7,2.645240785020183,0.07401050162380111,3.888392341499369,0.07354074633248234,-1.2431515564791862,0.10433501675729574,-1.2600000000000002 +7,3,19.156608143150834,0.07120096198862007,14.719995108422749,0.06876106182840862,4.436613034728083,0.09898313296655724,2.2100000000000004 diff --git a/summaries/jan_14_2026/fragments/p38/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/p38/dg_comparison_plot.png new file mode 100644 index 0000000..018dc49 Binary files /dev/null and b/summaries/jan_14_2026/fragments/p38/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/p38/dg_plot.png b/summaries/jan_14_2026/fragments/p38/dg_plot.png new file mode 100644 index 0000000..ab13c4b Binary files /dev/null and b/summaries/jan_14_2026/fragments/p38/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/p38/dg_results.csv b/summaries/jan_14_2026/fragments/p38/dg_results.csv new file mode 100644 index 0000000..b77d684 --- /dev/null +++ b/summaries/jan_14_2026/fragments/p38/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1_1W7H,Nc1ncccc1OCc1ccccc1,-3.2032798707811483,0.03491629655285727,-3.94 +3,c1ccc(COc2cccnc2)cc1,-3.2989186114559033,0.03399212921546534,-4.09 +4,Nc1ncccc1OCc1c(Cl)cccc1Cl,-5.066839495716071,0.04233885020275529,-5.4 +5_1WBW,Nc1ncccc1OCc1cccc2ccccc12,-4.8662629854054025,0.05008609366778338,-5.94 +6,OCCNc1ccc(OCc2c(Cl)cccc2Cl)cn1,-6.655501243022224,0.04599735706583777,-5.04 +7,CC(C)(CO)Nc1ccc(OCc2c(Cl)cccc2Cl)cn1,-7.6191977936192545,0.05067263672777963,-6.3 diff --git a/summaries/jan_14_2026/fragments/t4_lysozyme/README.md b/summaries/jan_14_2026/fragments/t4_lysozyme/README.md new file mode 100644 index 0000000..93b7b40 --- /dev/null +++ b/summaries/jan_14_2026/fragments/t4_lysozyme/README.md @@ -0,0 +1,39 @@ +# T4 Lysozyme Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.57 +- RMSE: 0.69 +- R²: 0.56 +- Kendall 𝜏: 0.48 +- Spearman ρ: 0.69 + +## System Details +- Ligands: 12 +- Host Atoms: 2609 +- Map Details: + - Edges: 22 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 6.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.03 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 1626.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/fragments/t4_lysozyme/ddg_results.csv b/summaries/jan_14_2026/fragments/t4_lysozyme/ddg_results.csv new file mode 100644 index 0000000..5925e0c --- /dev/null +++ b/summaries/jan_14_2026/fragments/t4_lysozyme/ddg_results.csv @@ -0,0 +1,23 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +butyl benzene,propyl benzene,-3.9147223776231614,0.04467195134391388,-3.3466949076269006,0.04379848453180378,-0.5680274699962606,0.06256109401341751,0.1500000000000011 +ethyl benzene,butyl benzene,5.362271756168281,0.04608949745687578,5.4991173840895495,0.04464779538482725,-0.13684562792126856,0.06416905335559159,-0.9400000000000012 +ethyl benzene,benzene,-0.012319538677255406,0.04697549574439555,-1.7070428715032218,0.046698604608702725,1.6947233328259663,0.06623788095064391,0.5599999999999996 +ethyl benzene,isobutyl benzene,5.3310961730653945,0.048404295792889275,5.786120064818608,0.04773391301489138,-0.45502389175321395,0.06798163209955124,-0.7200000000000009 +ethyl benzene,m-xylene,0.6010703019384638,0.053134162612989116,-2.127105117693387,0.05224999007522943,2.728175419631851,0.07452047168023794,0.9999999999999993 +butyl benzene,isobutyl benzene,-0.21873830026867824,0.056726790944756064,-0.20952590176435526,0.05270520194198119,-0.009212398504322988,0.07743233899757307,0.2200000000000003 +ethyl benzene,ortho methyl ethyl benzene,3.4609327120137703,0.04430208971675611,2.258979685872701,0.04500626346723302,1.2019530261410696,0.06315250513284094,1.1899999999999993 +ethyl benzene,o-xylene,1.6615717257227027,0.053603119206459174,-0.6689798432614293,0.05135689688300743,2.330551568984132,0.07423493278850415,1.1499999999999988 +ethyl benzene,para methyl ethyl benzene,-0.9580813189555365,0.04254310531305989,-0.007153451337082188,0.043212206587215994,-0.9509278676184543,0.06064000830981421,0.3399999999999993 +ethyl benzene,p-xylene,-1.6327209056173488,0.053162235919302005,-2.2532835513582703,0.05182243760753404,0.6205626457409212,0.07424141948754942,1.0899999999999996 +m-xylene,benzene,-0.12272487295794877,0.0512072165963982,-0.19314669631648937,0.050766127705307945,0.07042182335854061,0.07210671781285065,-0.4399999999999998 +meta methyl ethyl benzene,ethyl benzene,-1.627777495723018,0.04485508102140164,-0.1463786390056781,0.04417083958258197,-1.4813988567173397,0.06295269146642338,-0.6399999999999989 +methyl benzene,benzene,0.6028517382975919,0.043351808278734624,-0.08337106164455904,0.042695467932219885,0.686222799942151,0.06084638249713272,0.32000000000000073 +meta methyl ethyl benzene,ortho methyl ethyl benzene,1.7560461896247388,0.052689679585108035,1.8839769407095954,0.0517731830852982,-0.12793075108485652,0.07386924137667286,0.5500000000000004 +meta methyl ethyl benzene,para methyl ethyl benzene,-2.3034451340972053,0.04945814207300707,-0.20913787921466664,0.05111704334248971,-2.0943072548825388,0.07112706894981491,-0.29999999999999966 +methyl benzene,o-xylene,2.6787769929952168,0.04389876781915738,1.6163514198926425,0.043015793709080166,1.062425573102574,0.061461047212542905,0.9099999999999999 +methyl benzene,m-xylene,1.476847732260497,0.04464953146298633,0.15933714535058305,0.04272312482620181,1.317510586909914,0.06179681265874015,0.7600000000000005 +methyl benzene,p-xylene,-0.1655098604348872,0.042155125065313354,0.03093805839018169,0.043725372945701925,-0.19644791882506887,0.060736832387875916,0.8500000000000009 +ortho methyl ethyl benzene,o-xylene,-2.1453856629472043,0.04473518126081169,-2.841544537467029,0.04219511360379726,0.6961588745198244,0.06149523603072871,-0.04000000000000052 +p-xylene,para methyl ethyl benzene,0.629065185017479,0.03970112498207291,2.2449558237244314,0.03906194008952667,-1.6158906387069523,0.055695731330147234,-0.7500000000000003 +methyl benzene,propyl benzene,2.976833480641011,0.04579540381879237,4.436634002105582,0.044287684677791754,-1.4598005214645713,0.06370728392457,-1.029999999999999 +propyl benzene,isobutyl benzene,3.7220715468977863,0.043945715447174676,3.10146965792972,0.04574146984452987,0.6206018889680663,0.06343112776627956,0.0699999999999992 diff --git a/summaries/jan_14_2026/fragments/t4_lysozyme/dg_comparison_plot.png b/summaries/jan_14_2026/fragments/t4_lysozyme/dg_comparison_plot.png new file mode 100644 index 0000000..3548dbf Binary files /dev/null and b/summaries/jan_14_2026/fragments/t4_lysozyme/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/fragments/t4_lysozyme/dg_plot.png b/summaries/jan_14_2026/fragments/t4_lysozyme/dg_plot.png new file mode 100644 index 0000000..71b5beb Binary files /dev/null and b/summaries/jan_14_2026/fragments/t4_lysozyme/dg_plot.png differ diff --git a/summaries/jan_14_2026/fragments/t4_lysozyme/dg_results.csv b/summaries/jan_14_2026/fragments/t4_lysozyme/dg_results.csv new file mode 100644 index 0000000..31ea5e7 --- /dev/null +++ b/summaries/jan_14_2026/fragments/t4_lysozyme/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +butyl benzene,CCCCc1ccccc1,-6.276725164181708,0.04268408870427084,-6.66 +propyl benzene,CCCc1ccccc1,-6.811584118895263,0.035833811089610625,-6.51 +ethyl benzene,CCc1ccccc1,-6.130060876197083,0.019688119250384283,-5.72 +benzene,c1ccccc1,-4.270815439665617,0.0367539039623865,-5.16 +isobutyl benzene,CC(C)Cc1ccccc1,-6.351046101999265,0.038489208372803764,-6.44 +m-xylene,Cc1cccc(C)c1,-3.8669544884525866,0.038539612453492536,-4.72 +ortho methyl ethyl benzene,CCc1ccccc1C,-4.840001340836873,0.042145625555439915,-4.53 +o-xylene,Cc1ccccc1C,-4.037162153363832,0.03501001767867717,-4.57 +para methyl ethyl benzene,CCc1ccc(C)cc1,-6.994279719364908,0.03742609267822114,-5.38 +p-xylene,Cc1ccc(C)cc1,-5.399986521371384,0.035488476761139164,-4.63 +meta methyl ethyl benzene,CCc1cccc(C)c1,-4.7454561221901015,0.03732715175531717,-5.08 +methyl benzene,Cc1ccccc1,-5.1559279534813784,0.02527492466251799,-5.48 diff --git a/summaries/jan_14_2026/jacs_set/bace/README.md b/summaries/jan_14_2026/jacs_set/bace/README.md new file mode 100644 index 0000000..341bffa --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/bace/README.md @@ -0,0 +1,39 @@ +# Bace Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.63 +- RMSE: 1.86 +- R²: 0.02 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.05 + +## System Details +- Ligands: 36 +- Host Atoms: 6044 +- Map Details: + - Edges: 61 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 5.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 12.53 Hours +- Average Time Per Edge: 0.21 Hours +- Total Nanoseconds Simulated: 5516.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/bace/ddg_results.csv b/summaries/jan_14_2026/jacs_set/bace/ddg_results.csv new file mode 100644 index 0000000..6b41967 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/bace/ddg_results.csv @@ -0,0 +1,62 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +CAT-13a,CAT-13i,20.36863192748177,0.053612301052248096,20.64569420081112,0.05040069264252204,-0.27706227332935307,0.07358334487479391,-0.42999999999999877 +CAT-13a,CAT-13o,-8.395498875412915,0.05077561377487465,-9.240498307660816,0.0493833767641573,0.8449994322479001,0.07082994320798197,0.3000000000000005 +CAT-13b,CAT-13h,13.219274369425273,0.051618225762859675,17.133663060917886,0.049889384685068504,-3.9143886914926127,0.07178712931410684,-0.5099999999999998 +CAT-13b,CAT-13i,16.1211345782723,0.048395889090560765,17.17398393662119,0.047703288670729496,-1.052849358348891,0.0679541450602449,-0.15000000000000024 +CAT-13b,CAT-13k,4.933919335097621,0.06861449275299861,7.0641224054035305,0.0663528605354542,-2.13020307030591,0.09544972874235283,-0.5800000000000007 +CAT-13c,CAT-13f,21.38343123053319,0.061998396935919825,23.68322825115919,0.06120798591466872,-2.299797020626001,0.08712186156387017,0.2299999999999996 +CAT-13d,CAT-13a,-12.327079667322812,0.0510218439413275,-13.601833529488214,0.04998277246411101,1.2747538621654027,0.07142482833281626,1.6300000000000008 +CAT-13d,CAT-13c,-24.475572348654016,0.06152757273817647,-26.959622906028855,0.06124234327441343,2.484050557374839,0.08681167442684588,1.1500000000000012 +CAT-13d,CAT-13i,-20.050727568359935,0.06336684341472779,-21.263395023551013,0.05907520698313491,1.2126674551910765,0.0866327704996606,1.200000000000002 +CAT-13d,CAT-17d,-5.984152018781311,0.045972792542413564,-7.514706469614324,0.046347497912604736,1.5305544508330131,0.06528084111672196,1.0500000000000016 +CAT-13d,CAT-17i,-5.5152150325115405,0.04051696650753451,-5.939796962783487,0.04204904112947534,0.424581930271947,0.058393034129774264,1.000000000000001 +CAT-13e,CAT-13c,-56.59375107867699,0.07122248786976543,-58.27569967957302,0.06848908771438109,1.6819486008960296,0.09880990797641231,0.6399999999999998 +CAT-13e,CAT-13d,-28.87925212956247,0.0670758761010192,-27.802190766732163,0.06254496408906164,-1.0770613628303067,0.091711753268713,-0.5100000000000016 +CAT-13e,CAT-13f,-35.31503238573584,0.0722215818678441,-34.63579908121378,0.07175290168001291,-0.679233304522062,0.1018058730476553,0.8699999999999993 +CAT-13g,CAT-13m,-59.01360317405248,0.07407690434895083,-60.40742987635483,0.07218974135041575,1.3938267023023512,0.1034347451979437,0.3300000000000009 +CAT-13g,CAT-4p,-32.91649446301714,0.0727584901228666,-32.423626107158945,0.07164605191203038,-0.4928683558581862,0.10211246074569268,-0.9899999999999992 +CAT-13h,CAT-17a,-8.692096042786714,0.050651522253672615,-8.071914491377502,0.04962131093675964,-0.6201815514092115,0.07090734239623478,-1.1000000000000023 +CAT-13h,CAT-17i,-11.662154141733074,0.04991537305728123,-12.65628376931566,0.04881229244072734,0.9941296275825864,0.06981535906064398,0.15999999999999867 +CAT-13j,CAT-13g,36.27596539135046,0.07289737569231856,40.06837745442139,0.07166341134176338,-3.7924120630709246,0.10222363673811365,-0.35999999999999954 +CAT-13j,CAT-13o,-8.333734038391594,0.061918897625943436,-10.274179404214127,0.059748037558703386,1.9404453658225331,0.08604520832288277,0.19000000000000075 +CAT-13j,CAT-4i,0.2203445385025492,0.05265198093938015,2.9740768242708615,0.05434411811684956,-2.753732285768312,0.07566712807249228,0.470000000000001 +CAT-13j,CAT-4n,1.202902851243818,0.05146571193520992,5.164286268458445,0.054704470527702484,-3.961383417214627,0.07510857874247308,-0.35999999999999954 +CAT-13k,CAT-13m,-26.334910566461296,0.06272249906951588,-23.403147375043947,0.06309786392844795,-2.9317631914173514,0.08896882780984784,0.9400000000000003 +CAT-13k,CAT-4b,11.536232999938203,0.0539124172806435,16.291033405959503,0.051783378578043895,-4.7548004060213,0.07475337473318007,0.07000000000000091 +CAT-13k,CAT-4d,15.065597963044612,0.057522369091984805,19.900580949455918,0.05569928467695341,-4.8349829864113065,0.0800701770915915,0.5900000000000009 +CAT-13n,CAT-13m,-1.1294475172162295,0.04877080792914954,0.6681122395422137,0.04855184056003586,-1.7975597567584432,0.06881767889015974,-0.21999999999999945 +CAT-13n,CAT-13o,9.687128486714151,0.05962609267005716,8.638636923177378,0.05947744533526138,1.0484915635367738,0.08421898497789705,0.0 +CAT-13n,CAT-4i,23.6431782601415,0.05372608069134067,25.96547776957254,0.05419454986473039,-2.3222995094310424,0.07631212866571865,0.28000000000000025 +CAT-13o,CAT-13f,40.68512932989508,0.06889073026344536,45.074252064454896,0.07047524343726769,-4.38912273455982,0.09855299413905662,-0.5500000000000004 +CAT-17a,CAT-17h,-3.5879297381902866,0.0424383367939557,-4.3134927807141725,0.04185934086991272,0.7255630425238856,0.059608865514290406,0.4000000000000018 +CAT-17b,CAT-13d,-2.235617603656303,0.047912604828352315,-2.776509137682391,0.047187460068566625,0.5408915340260884,0.06724785564730239,-0.45000000000000245 +CAT-17b,CAT-17c,-1.4355804368552376,0.0514519187693025,-1.7401175044839157,0.051734406607541576,0.30453706762867805,0.07296402382049214,0.15999999999999867 +CAT-17b,CAT-17e,-1.3976589370417662,0.03697923660852472,-1.1257640415276884,0.03882421764711601,-0.27189489551407797,0.053617010510283857,0.0 +CAT-17c,CAT-17e,0.40539153293195096,0.05468541846094094,0.6223008366427789,0.054559937567876124,-0.21690930371082798,0.0772481830184941,-0.15999999999999867 +CAT-17d,CAT-17h,-0.45868402288901,0.04116283696727768,2.0451692631724905,0.042244128511863335,-2.5038532860615006,0.058982586760174455,-0.9099999999999999 +CAT-17f,CAT-17e,8.233605976898955,0.05225536503606593,8.69356681887379,0.05362052526256956,-0.4599608419748343,0.07487178309941844,-0.5999999999999993 +CAT-17f,CAT-24,-2.283528293785608,0.030393898738783297,1.1476203715693871,0.03358915220411088,-3.431148665354995,0.0452992298646935,-1.9269999999999996 +CAT-17g,CAT-17a,-0.668458212048748,0.05203121728279864,1.2942476063395667,0.04896132542144396,-1.9627058183883146,0.07144549642177832,-0.9900000000000009 +CAT-17g,CAT-17d,-3.922174063860023,0.04279160649017624,-4.6983488252059535,0.04064148299036278,0.7761747613459303,0.059015690504018,0.32000000000000073 +CAT-17g,CAT-17f,-7.9633211584010475,0.032816109323989345,-6.9386554318944045,0.035460353288689746,-1.0246657265066434,0.04831494268363267,0.32000000000000073 +CAT-17g,CAT-24,-9.517065553301856,0.040782404332347484,-5.678756292419948,0.04075345297401355,-3.838309260881908,0.057654561245682974,-1.6069999999999989 +CAT-17i,CAT-17h,-0.1643966198290856,0.036816294252717784,0.302521516220775,0.0362633277325551,-0.4669181360498606,0.05167657555161139,-0.8599999999999992 +CAT-24,CAT-17c,10.374016340490003,0.04340395897653573,7.1077534730912735,0.04332784862691497,3.26626286739873,0.061328672914662465,1.486999999999999 +CAT-4a,CAT-4c,0.888324551005565,0.050596786235954275,1.0931429576154514,0.047326385061012013,-0.20481840660988646,0.06928074408051657,0.08000000000000104 +CAT-4a,CAT-4k,-10.790624904700957,0.034861890257972046,-12.342086960862238,0.038086903417461716,1.5514620561612815,0.051632970128493896,0.08000000000000104 +CAT-4a,CAT-4l,1.9454532891335492,0.043453504184416215,1.3355188912912466,0.044444887579864395,0.6099343978423026,0.06215750202422764,-1.4099999999999995 +CAT-4b,CAT-4d,4.672281432404466,0.0486104450295598,4.317119840061291,0.04441052361606358,0.3551615923431753,0.06584276705777785,0.5199999999999999 +CAT-4c,CAT-13k,-11.671328244858067,0.06048362724257322,-15.159422264534403,0.05867151793457633,3.488094019676336,0.08426515401496551,-1.85 +CAT-4c,CAT-4o,-5.54533851192575,0.05838709432199912,-4.523553502196265,0.0557324921286139,-1.0217850097294847,0.0807165625025746,-1.5299999999999994 +CAT-4j,CAT-4o,3.9345303334652275,0.040234680890842,4.580742360816778,0.041737657951581096,-0.6462120273515506,0.05797293883935044,-0.35999999999999954 +CAT-4k,CAT-4j,2.9850702728914498,0.04142484119005699,4.0806872641153715,0.042147668368506336,-1.095616991223922,0.05909689853556641,-1.17 +CAT-4k,CAT-4l,14.14478914308897,0.04589140497890118,13.669162889914505,0.048405682639033776,0.4756262531744649,0.06670180779175608,-1.4900000000000007 +CAT-4l,CAT-13k,-13.909811181235803,0.05315751126832793,-15.677637065535267,0.052898091863818726,1.7678258842994636,0.07499286050735374,-0.35999999999999954 +CAT-4m,CAT-13k,-2.5834897846594362,0.04749540161409252,-7.592825515651012,0.04883161809014854,5.009335730991576,0.06812004183634993,-0.5499999999999986 +CAT-4m,CAT-4j,0.15665973897780303,0.04677072121649156,-1.3714141565662936,0.04386789389748201,1.5280738955440967,0.06412403978315397,0.13000000000000167 +CAT-4m,CAT-4o,4.34161919525961,0.037846207364387374,3.456138288602525,0.034014437908405755,0.885480906657085,0.05088533578638348,-0.22999999999999787 +CAT-4n,CAT-13k,-0.16492993913695975,0.059427292853281175,-4.548377715333636,0.06020705532598023,4.383447776196677,0.08459605574076895,-0.6099999999999994 +CAT-4n,CAT-4p,3.252679809502729,0.04360153331491561,3.7617429304271934,0.04466158395380949,-0.5090631209244645,0.06241594979390179,-0.9899999999999992 +CAT-4o,CAT-4b,3.6459033154485847,0.045192973440909764,5.096156901531465,0.04300251478175835,-1.4502535860828802,0.06238285923221315,-0.24999999999999983 +CAT-4o,CAT-4d,7.459167421143917,0.04875179336258171,8.816226095353949,0.04794647678568519,-1.357058674210032,0.06837837371733928,0.2700000000000001 +CAT-4p,CAT-4i,-4.663788594342449,0.049984847079025445,-5.817928463142708,0.04984304617048361,1.1541398688002589,0.07058905148156136,1.8199999999999998 diff --git a/summaries/jan_14_2026/jacs_set/bace/dg_comparison_plot.png b/summaries/jan_14_2026/jacs_set/bace/dg_comparison_plot.png new file mode 100644 index 0000000..fb210d0 Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/bace/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/bace/dg_plot.png b/summaries/jan_14_2026/jacs_set/bace/dg_plot.png new file mode 100644 index 0000000..023d9af Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/bace/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/bace/dg_results.csv b/summaries/jan_14_2026/jacs_set/bace/dg_results.csv new file mode 100644 index 0000000..aa21927 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/bace/dg_results.csv @@ -0,0 +1,37 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CAT-13a,CN1C(=O)[C@@](C)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-7.123468341280589,0.05023700113012523,-8.843 +CAT-13i,CN1C(=O)[C@@](CC2CC2)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-7.212864835786117,0.049640577872482036,-9.273 +CAT-13o,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(c2nccs2)[NH+]=C1N,-6.065473541374435,0.054341667392835,-8.543 +CAT-13b,CC[C@]1(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C(N)N(C)C1=O,-5.77471628832193,0.052578636935812814,-9.123 +CAT-13h,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2(C)CC2)[NH+]=C1N,-9.595144719852374,0.06167238281692101,-9.633 +CAT-13k,CN1C(=O)[C@@](c2cccnc2)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-7.310852635093523,0.04758901691596171,-9.703 +CAT-13c,CC(C)[C@]1(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C(N)N(C)C1=O,-6.661269728636178,0.0652701374569858,-9.323 +CAT-13f,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CCCC2)[NH+]=C1N,-9.408913445454637,0.07324933310471995,-9.093 +CAT-13d,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CC2)[NH+]=C1N,-8.791627569059019,0.04637080952346065,-10.473 +CAT-17d,CN1C(=O)[C@](c2cccc(-c3cccnc3)c2)(C2CC2)[NH+]=C1N,-7.106102507681357,0.058404245520189434,-9.423 +CAT-17i,Cc1cncc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-8.636884877711257,0.053957258016364626,-9.473 +CAT-13e,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CCC2)[NH+]=C1N,-8.22536387654516,0.06449412516343114,-9.963 +CAT-13g,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(C2CCCCC2)[NH+]=C1N,-11.393287772086518,0.07607049728394334,-9.093 +CAT-13m,CN1C(=O)[C@@](c2cncnc2)(c2cccc(-c3cccc(Cl)c3)c2)[NH+]=C1N,-9.897919565812783,0.0667460239152856,-8.763 +CAT-4p,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cncc(Cl)c3)c2)[NH+]=C1N,-11.865010829010862,0.07643948640277301,-10.083 +CAT-17a,CN1C(=O)[C@](c2cccc(-c3cc(Cl)cc(Cl)c3)c2)(C2CC2)[NH+]=C1N,-10.08665431772533,0.065119897302302,-10.733 +CAT-13j,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(c2ccccn2)[NH+]=C1N,-7.721244619305211,0.0696001274835739,-8.733 +CAT-4i,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3ccccn3)c2)[NH+]=C1N,-10.46624937841266,0.06717678607304856,-8.263 +CAT-4n,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cncc(C#N)c3)c2)[NH+]=C1N,-11.53930165139996,0.06848113870116533,-9.093 +CAT-4b,COc1cccc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)c1,-12.432178994644728,0.06846522244762113,-9.633 +CAT-4d,CCOc1cccc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)c1,-12.23014566356786,0.06776876028086948,-9.113 +CAT-13n,CN1C(=O)[C@](c2cccc(-c3cccc(Cl)c3)c2)(c2ncccn2)[NH+]=C1N,-7.849177487992479,0.059154299785624656,-8.543 +CAT-17h,CN1C(=O)[C@](c2cccc(-c3cncc(Cl)c3)c2)(C2CC2)[NH+]=C1N,-9.334789889261687,0.057566074096012755,-10.333 +CAT-17b,COc1cccc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-9.22154067222384,0.07136984184558436,-10.023 +CAT-17c,CN1C(=O)[C@](c2cccc(-c3cccc(C#N)c3)c2)(C2CC2)[NH+]=C1N,-8.982778191541156,0.08183490572955172,-9.863 +CAT-17e,COc1cncc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-9.387369437445718,0.0777754155246856,-10.023 +CAT-17f,CN1C(=O)[C@](c2cccc(-c3cncc(C#N)c3)c2)(C2CC2)[NH+]=C1N,-8.896893458817372,0.06902758396168544,-9.423 +CAT-24,CC#Cc1cncc(-c2cccc([C@@]3(C4CC4)[NH+]=C(N)N(C)C3=O)c2)c1,-12.177213706277625,0.07314586415449958,-11.35 +CAT-17g,CN1C(=O)[C@](c2cccc(-c3cncc(F)c3)c2)(C2CC2)[NH+]=C1N,-8.031099899556052,0.06283707578434011,-9.743 +CAT-4a,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3ccccc3)c2)[NH+]=C1N,-10.340664793707912,0.06542161128010004,-7.933000000000001 +CAT-4c,COc1ccc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)cc1,-10.473731664611073,0.06812909067463434,-7.853 +CAT-4k,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3ccncc3)c2)[NH+]=C1N,-9.188656945966551,0.06517179312593012,-7.853 +CAT-4l,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cnccn3)c2)[NH+]=C1N,-9.209590754676508,0.06496641911873045,-9.343 +CAT-4o,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cncc(F)c3)c2)[NH+]=C1N,-11.099722152258561,0.06464064935317497,-9.383 +CAT-4j,CN1C(=O)[C@@](c2ccccc2)(c2cccc(-c3cccnc3)c2)[NH+]=C1N,-10.417777861291073,0.06400617317535952,-9.023 +CAT-4m,Cc1cncc(-c2cccc([C@@]3(c4ccccc4)[NH+]=C(N)N(C)C3=O)c2)c1,-12.059317925609868,0.06446193791876048,-9.153 diff --git a/summaries/jan_14_2026/jacs_set/cdk2/README.md b/summaries/jan_14_2026/jacs_set/cdk2/README.md new file mode 100644 index 0000000..48d1814 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/cdk2/README.md @@ -0,0 +1,39 @@ +# Cdk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.68 +- RMSE: 0.88 +- R²: 0.56 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.76 + +## System Details +- Ligands: 16 +- Host Atoms: 9028 +- Map Details: + - Edges: 28 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 5.9 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.28 Hours +- Average Time Per Edge: 0.26 Hours +- Total Nanoseconds Simulated: 2654.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/cdk2/ddg_results.csv b/summaries/jan_14_2026/jacs_set/cdk2/ddg_results.csv new file mode 100644 index 0000000..60b2cef --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/cdk2/ddg_results.csv @@ -0,0 +1,29 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +17,1h1q,1.2980183369559701,0.044100481731450855,0.5125029808609463,0.043922001324217676,0.7855153560950238,0.06224142261605698,-1.1399999999999986 +17,1oi9,-8.432247994865003,0.05268424796761688,-7.709811061886753,0.052235779467340517,-0.7224369329782506,0.07419034061435474,-2.7 +17,1oiu,-61.03916914668565,0.04750818542881563,-58.18587485935045,0.04539707870766377,-2.8532942873352063,0.06571090044983822,-2.04 +1h1r,1h1q,2.2036223028753854,0.044288615393204785,0.8061943844240054,0.042398808276961214,1.39742791845138,0.06131182917475005,-0.5099999999999998 +1h1r,1oi9,-7.707067698007003,0.05263769761835551,-7.313512045529158,0.052461623839047636,-0.39355565247784524,0.07431654719099347,-2.070000000000001 +1h1r,1oiu,-59.48922595041891,0.04894408404559137,-57.97712929881034,0.04599406502866861,-1.5120966516085728,0.06716381005365396,-1.4100000000000013 +1h1s,29,48.57182547968636,0.06148612881983624,47.76196348691784,0.05953898430964331,0.809861992768522,0.08558875329080012,1.369999999999999 +1h1s,31,42.381713930703825,0.05547625674162317,40.53155996875929,0.05529662525280128,1.850153961944537,0.07832835901773527,1.71 +1h1s,32,10.604978021955182,0.05304863303674739,8.217655981147377,0.04975595498447927,2.3873220408078053,0.0727310973620295,1.4999999999999991 +1oiu,1h1q,62.267009846625186,0.057012550569810264,58.79208961256965,0.056371109680457845,3.474920234055539,0.08017563800233447,0.9000000000000015 +1oiy,1oi9,7.065252671864454,0.05197519929538134,7.460383103053372,0.04736833726375895,-0.39513043118891805,0.07032197890366726,0.04999999999999895 +1oiy,26,13.23647464174959,0.052438016095713684,12.464154285727417,0.05141557161204591,0.772320356022173,0.07343913490944558,1.359999999999999 +1oiy,29,11.413739544036032,0.06579218446425787,11.565315760229762,0.06507367362252828,-0.1515762161937286,0.09253753041501737,-0.09000000000000116 +1oiy,31,1.2100173527488784,0.06864620980420472,0.31609208551646806,0.06709561606364281,0.8939252672324105,0.09599022770804669,0.24999999999999983 +20,1h1q,6.68984908255064,0.0500665801282873,5.490315081618288,0.04675392110297604,1.1995340009323514,0.06850249327028558,0.5400000000000019 +21,1h1q,-1.3925562856197742,0.05173238077547823,-1.5672235391265326,0.050162916729599605,0.1746672535067584,0.07205940213129591,-0.3499999999999994 +21,20,-6.211032806679643,0.05191086601815336,-6.276718069868379,0.05017195270220448,0.06568526318873588,0.07219392528950695,-0.8900000000000013 +22,20,-7.795553334200136,0.04799648383242985,-5.593049444191944,0.04631699835686604,-2.2025038900081917,0.06670027583950934,-0.860000000000001 +22,21,0.20620898001141125,0.05350599595518763,1.4181068090209543,0.05207246106239604,-1.211897829009543,0.07466212429506212,0.030000000000000387 +22,32,-53.72170104349059,0.06552847739349743,-50.717750711931906,0.0662159722629689,-3.003950331558682,0.09315866214282152,-1.8900000000000008 +26,1h1q,0.14859412036362069,0.05101835033988496,-1.396740123302513,0.049011846779835534,1.5453342436661337,0.0707462592380213,0.25000000000000155 +26,1oi9,-10.235828582569852,0.045195342846127515,-9.499756662221602,0.0416069475048112,-0.7360719203482499,0.06143091319235882,-1.31 +28,1h1s,-23.698593639131573,0.05232369370615869,-24.15704058139669,0.05082328175773839,0.4584469422651172,0.07294364188661254,-0.14000000000000012 +28,1oiy,13.123032996690732,0.06734755371061399,10.918349465128694,0.06645906161830241,2.2046835315620386,0.09461765090081951,1.32 +28,30,15.732519830829187,0.050625662463164044,13.805192783266586,0.05054749158321948,1.9273270475626008,0.07154024465424941,1.2999999999999998 +30,29,13.614515961371646,0.06309418817965642,13.919772505508028,0.0594719095893761,-0.3052565441363824,0.0867051590867396,-0.07000000000000091 +30,31,4.4696631522271835,0.04618414832393044,2.779594083925843,0.0472736353385092,1.6900690683013402,0.06608912281552201,0.2700000000000001 +30,32,-30.297511753403814,0.0600789818005507,-30.307575825295746,0.05890743073808391,0.010064071891931524,0.08414017738484425,0.05999999999999908 diff --git a/summaries/jan_14_2026/jacs_set/cdk2/dg_comparison_plot.png b/summaries/jan_14_2026/jacs_set/cdk2/dg_comparison_plot.png new file mode 100644 index 0000000..2810294 Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/cdk2/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/cdk2/dg_plot.png b/summaries/jan_14_2026/jacs_set/cdk2/dg_plot.png new file mode 100644 index 0000000..0019f2d Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/cdk2/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/cdk2/dg_results.csv b/summaries/jan_14_2026/jacs_set/cdk2/dg_results.csv new file mode 100644 index 0000000..35ac3b2 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/cdk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,Brc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.339430006732549,0.04636798505109418,-7.04 +1h1q,c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-7.4893179572496695,0.03902112451020986,-8.18 +1oi9,Oc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.488647263326845,0.03703917075827829,-9.74 +1oiu,NS(=O)(=O)c1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-10.929923969709002,0.05036299306084047,-9.08 +1h1r,Clc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-9.119196955812477,0.05229110252070823,-7.669999999999999 +1h1s,NS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-10.922299737624263,0.05021871889241533,-11.25 +29,CN(C)S(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.893541215220832,0.05736641785405363,-9.88 +31,C[S@](=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.44847788598934,0.055643713001321864,-9.54 +32,COc1cc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)ccc1S(N)(=O)=O,-9.096943486712036,0.05135588718178224,-9.75 +1oiy,NC(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.391595567846277,0.0379640662350761,-9.79 +26,COc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.801241452355837,0.04481664603412828,-8.43 +20,OCc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.36544129098689,0.04942540468420637,-8.72 +21,COc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.884056577655194,0.054629162180451496,-7.829999999999999 +22,CSc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-6.323298409094201,0.044324502087033764,-7.86 +28,CNS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.515352106120648,0.05660874729722065,-11.11 +30,CS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.67123611756395,0.05657354775310943,-9.81 diff --git a/summaries/jan_14_2026/jacs_set/jnk1/README.md b/summaries/jan_14_2026/jacs_set/jnk1/README.md new file mode 100644 index 0000000..050bfc6 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/jnk1/README.md @@ -0,0 +1,39 @@ +# Jnk1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.06 +- RMSE: 1.18 +- R²: 0.56 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.76 + +## System Details +- Ligands: 21 +- Host Atoms: 5993 +- Map Details: + - Edges: 36 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 13 + - Mean Dummy Atoms: 6.5 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.21 Hours +- Average Time Per Edge: 0.20 Hours +- Total Nanoseconds Simulated: 3251.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/jnk1/ddg_results.csv b/summaries/jan_14_2026/jacs_set/jnk1/ddg_results.csv new file mode 100644 index 0000000..0c5e7a4 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/jnk1/ddg_results.csv @@ -0,0 +1,37 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +17124-1,18631-1,-3.984746586958577,0.055019311155190945,-5.742032697207315,0.054643052168358935,1.7572861102487378,0.0775434571725153,0.2700000000000001 +17124-1,18637-1,-8.544059879851588,0.05960966305377047,-8.416369981841548,0.05807175895645857,-0.12768989801003863,0.08322043689912396,-0.46000000000000085 +17124-1,18652-1,-15.316684431815421,0.05605101180221789,-14.40013760212952,0.05720918578340066,-0.9165468296859008,0.08009124085723744,-0.9999999999999993 +17124-1,18660-1,-31.443777798691546,0.06591442351877358,-30.81270056661522,0.06391247811041902,-0.6310772320763283,0.09181239614576586,0.9800000000000008 +18626-1,18628-1_flip,2.2876901314134375,0.05126797211863141,1.1589982306618696,0.05164968830376238,1.128691900751568,0.07277427613540774,0.1700000000000005 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+18628-1_flip,18625-1,-4.057473363258007,0.055915666865979326,-3.137616642121515,0.05369155997511879,-0.9198567211364918,0.0775199678381574,0.5899999999999992 +18629-1,18624-1,0.5741194642065184,0.04368046580801198,-0.0391481629672369,0.04259906150013544,0.6132676271737553,0.06101363072213639,0.18000000000000063 +18629-1,18635-1,1.6462517746466279,0.04549968085063947,0.6911785722827541,0.045855224549499335,0.9550732023638738,0.06459816232676478,1.3800000000000001 +18629-1,18636-1,-3.8652126937047036,0.05385431133031036,-3.20132721230372,0.052962339938805135,-0.6638854814009834,0.07553341181659642,1.1600000000000006 +18630-1,18624-1,0.4432010510395076,0.04387436288135955,0.08062885474085707,0.043461733682778045,0.3625721962986505,0.06175663537594923,0.6500000000000016 +18630-1,18633-1,1.695936219052999,0.041524971556422666,2.042568244538803,0.03883546717443729,-0.34663202548580435,0.05685522643889924,-0.02999999999999869 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+18634-1,18637-1,-9.511052642402225,0.057524805684171065,-8.478923855357277,0.05609555445854134,-1.0321287870449476,0.08034808335618727,-0.15000000000000024 +18634-1,18658-1,-4.8979526718618125,0.0401951089024481,-5.188205461754726,0.04040055343696203,0.2902527898929133,0.05698992452787148,0.29000000000000037 +18636-1,18624-1,4.5744919704961475,0.050871424936827093,2.784601576955551,0.051786174619192375,1.7898903935405963,0.07259276655971116,-0.98 +18636-1,18635-1,5.911844612721697,0.049318591198017764,4.4121890442590255,0.04918764631894905,1.4996555684626716,0.06965449007892612,0.21999999999999945 +18638-1,18634-1,19.996050362564375,0.05784570259024487,19.396169873907407,0.05797306642876476,0.5998804886569671,0.08189628648060322,0.0999999999999996 +18638-1,18639-1,76.15273001884411,0.06492708877459294,76.21304560211048,0.0636932621010824,-0.06031558326637706,0.09095250680339192,0.3499999999999994 +18638-1,18652-1,5.065489705896692,0.04813449207614218,5.744453624367953,0.045673523964085055,-0.6789639184712607,0.06635510619934269,-0.5899999999999992 +18639-1,18637-1,-75.63434084467642,0.06441529008296039,-75.70243257058239,0.06427004225514882,0.0680917259059715,0.09099432909775504,-0.4000000000000001 +18639-1,18652-1,-71.1899478080318,0.07141155179602736,-70.47856383770824,0.06971472530787495,-0.7113839703235759,0.09979856038375083,-0.9399999999999986 +18658-1,18660-1,-25.25298362445282,0.0640694521745736,-24.99800996384611,0.062370245829769376,-0.25497366060671267,0.08941444104179054,1.000000000000001 +18659-1,18634-1,-0.2292302630588176,0.05431518390116755,0.19687448736997798,0.05051029789974387,-0.4261047504287956,0.07417162123169833,-0.5199999999999999 +18659-1,18658-1,-5.197930379158135,0.05499658721224526,-5.6709120962881,0.053025713683295325,0.472981717129965,0.07639601374821144,-0.2299999999999996 +18659-1,18660-1,-21.71561093160938,0.06038570249004064,-20.58195514693802,0.059053125961532726,-1.1336557846713566,0.08446126183668079,0.7700000000000015 diff --git a/summaries/jan_14_2026/jacs_set/jnk1/dg_comparison_plot.png b/summaries/jan_14_2026/jacs_set/jnk1/dg_comparison_plot.png new file mode 100644 index 0000000..5c994d6 Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/jnk1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/jnk1/dg_plot.png b/summaries/jan_14_2026/jacs_set/jnk1/dg_plot.png new file mode 100644 index 0000000..c32072b Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/jnk1/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/jnk1/dg_results.csv b/summaries/jan_14_2026/jacs_set/jnk1/dg_results.csv new file mode 100644 index 0000000..3fd3249 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/jnk1/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17124-1,CCOc1nc(NC(=O)Cc2cc(OC)c(Br)cc2OC)cc(N)c1C#N,-10.76784471291233,0.04990212799813725,-9.68 +18631-1,CCOc1nc(NC(=O)Cc2ccccc2OC)cc(N)c1C#N,-8.847935561802391,0.03597112243884638,-9.41 +18637-1,CCOc1nc(NC(=O)Cc2cc(OC)c(NC(C)=O)cc2OC)cc(N)c1C#N,-11.208442533457102,0.05520275146634023,-10.14 +18652-1,COc1cc(S(C)(=O)=O)c(OC)cc1CC(=O)Nc1cc(N)c(C#N)c(OC(C)C)n1,-11.780798583160362,0.05488361361497855,-10.68 +18660-1,COc1ccc(OC)c(CC(=O)Nc2cc(N)c(C#N)c(OCCS(C)(=O)=O)n2)c1,-11.11935638669524,0.05757082762344989,-8.7 +18626-1,CCOc1nc(NC(=O)Cc2cccc(Cl)c2)cc(N)c1C#N,-7.9738941178689835,0.05129560345744796,-8.87 +18628-1_flip,CCOc1nc(NC(=O)Cc2ccccc2C)cc(N)c1C#N,-6.840287446760193,0.04809161270467041,-8.7 +18632-1,CCOc1nc(NC(=O)Cc2cccc(OC)c2)cc(N)c1C#N,-7.9397757225671315,0.04124954959069358,-9.08 +18635-1,CCOc1nc(NC(=O)Cc2cc(C)ccc2C)cc(N)c1C#N,-6.932451531970718,0.04879077963457808,-7.29 +18627-1,CCOc1nc(NC(=O)Cc2ccc(Cl)cc2)cc(N)c1C#N,-7.778590561597032,0.05088527241047263,-8.48 +18625-1,CCOc1nc(NC(=O)Cc2ccccc2Cl)cc(N)c1C#N,-7.830092484263096,0.04891222620639985,-8.11 +18630-1,CCOc1nc(NC(=O)Cc2ccc(C)cc2)cc(N)c1C#N,-7.445279624148252,0.04097663491103544,-9.14 +18633-1,CCOc1nc(NC(=O)Cc2ccc(OC)cc2)cc(N)c1C#N,-7.829589587033039,0.04804993840039135,-9.17 +18624-1,CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N,-7.044865788134792,0.03376319064018475,-8.49 +18629-1,CCOc1nc(NC(=O)Cc2cccc(C)c2)cc(N)c1C#N,-7.803895464227815,0.04927965930815641,-8.67 +18636-1,CCOc1nc(NC(=O)Cc2cc(Br)ccc2Br)cc(N)c1C#N,-8.576834149118563,0.049951418323119036,-7.51 +18634-1,CCOc1nc(NC(=O)Cc2cc(OC)ccc2OC)cc(N)c1C#N,-10.542300297142699,0.03340618214804289,-9.99 +18658-1,COc1ccc(OC)c(CC(=O)Nc2cc(N)c(C#N)c(OCCO)n2)c1,-10.255998898657063,0.04797738867421783,-9.7 +18638-1,CCOc1nc(NC(=O)Cc2cc(OC)c(S(C)(=O)=O)cc2OC)cc(N)c1C#N,-11.118576298516937,0.05801543506550756,-10.09 +18639-1,CCOc1nc(NC(=O)Cc2cc(OC)c([N+](=O)[O-])cc2OC)cc(N)c1C#N,-11.181232500807457,0.06378052422944992,-9.74 +18659-1,COCCOc1nc(NC(=O)Cc2cc(OC)ccc2OC)cc(N)c1C#N,-10.29195774915881,0.05274259963698922,-9.47 diff --git a/summaries/jan_14_2026/jacs_set/mcl1/README.md b/summaries/jan_14_2026/jacs_set/mcl1/README.md new file mode 100644 index 0000000..1923159 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/mcl1/README.md @@ -0,0 +1,39 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.98 +- RMSE: 1.35 +- R²: 0.54 +- Kendall 𝜏: 0.57 +- Spearman ρ: 0.75 + +## System Details +- Ligands: 42 +- Host Atoms: 2428 +- Map Details: + - Edges: 73 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 13.80 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 7271.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/mcl1/ddg_results.csv b/summaries/jan_14_2026/jacs_set/mcl1/ddg_results.csv new file mode 100644 index 0000000..a53ac44 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/mcl1/ddg_results.csv @@ -0,0 +1,74 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +23,44,4.7617022467217405,0.06172273766820857,4.204404756820407,0.0613885505351874,0.557297489901334,0.08705314745642315,0.16000000000000036 +23,51,9.63206631852366,0.06219775153714805,7.822112251578505,0.0611983082715464,1.8099540669451555,0.08725705261797483,0.3800000000000015 +23,54,3.2177484931703804,0.060127079413757695,4.249032046801713,0.060860183747652175,-1.0312835536313325,0.08555248473671767,-0.9499999999999987 +23,57,14.893847409844195,0.058407382743663826,14.793633872026069,0.05780416429031398,0.10021353781812724,0.08217507997115944,-0.20999999999999933 +23,62,5.608987844292699,0.04774128673415955,3.5510846459233587,0.04760141940208668,2.05790319836934,0.06741754658934566,0.8700000000000011 +23,64,-1.6834182748822653,0.0427388361478601,-0.5724290217978466,0.04353733225095869,-1.1109892530844188,0.06100907649525602,-0.6700000000000002 +23,66,-1.3386459366225214,0.040517034633585705,0.1849951762188883,0.044058064670943343,-1.5236411128414096,0.05985602023228916,0.4000000000000001 +23,68,16.046961595029583,0.059349115551397755,14.691155189533934,0.057598473553274576,1.3558064054956485,0.08270369805758648,1.1399999999999995 +26,57,-0.29864405597305826,0.043275855880048196,-0.4194391802690507,0.047725611480016694,0.12079512429599241,0.06442463576375271,-0.8000000000000002 +26,62,-9.070886322240636,0.060082696241006046,-11.62203783135975,0.059278947940173105,2.551151509119113,0.08440334150069388,0.28000000000000025 +26,64,-16.464988598607142,0.05793979727871601,-15.760597357672228,0.05745126772094112,-0.7043912409349145,0.08159453579402214,-1.2600000000000011 +26,66,-15.782894093512784,0.058141382299217115,-14.836431082230646,0.05721130819636727,-0.9464630112821364,0.08156932095588046,-0.19000000000000075 +26,68,0.5815448219960605,0.04115742388544444,-0.3602305688988004,0.040542962433980374,0.941775390894861,0.057772531049014086,0.5499999999999986 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--git a/summaries/jan_14_2026/jacs_set/mcl1/dg_plot.png b/summaries/jan_14_2026/jacs_set/mcl1/dg_plot.png new file mode 100644 index 0000000..8b40b1d Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/mcl1/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/mcl1/dg_results.csv b/summaries/jan_14_2026/jacs_set/mcl1/dg_results.csv new file mode 100644 index 0000000..b0a6ae4 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/mcl1/dg_results.csv @@ -0,0 +1,43 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +23,O=C([O-])c1sc2ccccc2c1CCCOc1cccc2ccccc12,-8.894332001961873,0.06063395045722162,-8.83 +44,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-8.697752527181477,0.05288873495314925,-8.67 +51,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-7.270707860734108,0.07817567938508643,-8.45 +54,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-9.510192247375217,0.07399001926075625,-9.78 +57,Cn1c(C(=O)[O-])c(CCCOc2cccc3ccccc23)c2ccccc21,-8.942046837980836,0.06873483480588377,-9.04 +62,O=C([O-])c1sc2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-6.733009953859958,0.0757908442445748,-7.959999999999999 +64,O=C([O-])c1sc2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-9.964706522804747,0.0808452433876309,-9.5 +66,O=C([O-])c1sc2c(Cl)cccc2c1CCCOc1cccc2ccccc12,-10.2307979178234,0.0745264693528223,-8.43 +68,O=C([O-])c1oc2ccc(Cl)cc2c1CCCOc1cccc2ccccc12,-7.871551506164492,0.074135576956536,-7.690000000000001 +26,O=C([O-])c1oc2ccccc2c1CCCOc1cccc2ccccc12,-9.08246687637069,0.06958060412186114,-8.24 +27,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1,-6.07807788283099,0.04705974154642996,-6.12 +31,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(C(F)(F)F)c1,-7.629903439758922,0.0532343545981626,-7.920000000000001 +32,Cc1ccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc1,-6.575724504606831,0.06516569020284749,-6.58 +38 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(-c2ccccc2)c1,-9.034218304835942,0.055779344869012475,-7.02 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+37,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc(C)c1Cl,-9.017859647308443,0.06483173803633244,-8.95 +34,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(C(F)(F)F)cc1,-7.37690542377065,0.07158882240321793,-6.87 +46 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2c(c1)CCC2,-6.299674450064242,0.08009310759277298,-7.6 +43 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ccccc2c1,-5.87341685141984,0.0757410678446755,-7.03 +47 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ncccc2c1,-4.504229761331496,0.07696866601111296,-5.78 +35,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-8.106886777243611,0.05190012563959209,-8.81 +36,CCc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-9.533978572204102,0.0664052736688907,-8.18 +52,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)ccc1Cl,-9.367226875507237,0.060270694527979556,-9.23 +49,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)ccc1Cl,-8.036886496213768,0.06387463081291063,-8.36 +50,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)cc(C)c1Cl,-8.4735605143696,0.06256018622375879,-9.33 +65,Cc1cc(OCCCc2c(C(=O)[O-])sc3c(Cl)cccc23)cc(C)c1Cl,-11.034993983719465,0.07130335901542298,-8.41 +61,Cc1cc(OCCCc2c(C(=O)[O-])sc3cccc(Cl)c23)cc(C)c1Cl,-8.875473502858501,0.06496534284300251,-8.08 +53,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)cc(C)c1Cl,-10.25369603008628,0.06927601267889032,-9.96 +58,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3cc(Cl)ccc23)cc(C)c1Cl,-11.203557278864205,0.07372476227772375,-9.41 +63,Cc1cc(OCCCc2c(C(=O)[O-])sc3cc(Cl)ccc23)cc(C)c1Cl,-10.733206543177724,0.0710649010004541,-9.06 +56,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3ccccc23)cc(C)c1Cl,-9.958769058283433,0.07348928199033677,-9.26 +60,Cc1cc(OCCCc2c(C(=O)[O-])sc3ccccc23)cc(C)c1Cl,-9.894417020966497,0.06330373415807296,-8.92 +67,Cc1cc(OCCCc2c(C(=O)[O-])oc3ccccc23)cc(C)c1Cl,-9.924446456207345,0.07202744118933076,-7.58 diff --git a/summaries/jan_14_2026/jacs_set/p38/README.md b/summaries/jan_14_2026/jacs_set/p38/README.md new file mode 100644 index 0000000..365d6db --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/p38/README.md @@ -0,0 +1,39 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.96 +- RMSE: 1.15 +- R²: 0.43 +- Kendall 𝜏: 0.45 +- Spearman ρ: 0.65 + +## System Details +- Ligands: 34 +- Host Atoms: 5651 +- Map Details: + - Edges: 60 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 22 + - Mean Dummy Atoms: 9.6 + - Median Dummy Atoms: 9.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 16.14 Hours +- Average Time Per Edge: 0.27 Hours +- Total Nanoseconds Simulated: 7202.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/p38/ddg_results.csv b/summaries/jan_14_2026/jacs_set/p38/ddg_results.csv new file mode 100644 index 0000000..eb96752 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/p38/ddg_results.csv @@ -0,0 +1,61 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +2aa,2y,12.126295156256022,0.06619396033138213,12.778327309123517,0.06462945381643889,-0.652032152867495,0.09251273796058464,-0.5099999999999998 +2aa,2z,7.937975498702852,0.06152207228165555,8.808249135097283,0.060096987881362064,-0.8702736363944299,0.08600356579957502,-1.0900000000000005 +2aa,3flw,22.20991574769434,0.06240429553479326,24.833181721012657,0.06100183072750355,-2.623265973318322,0.08726694364592365,-1.4099999999999995 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0000000..dfd308c Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/p38/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/p38/dg_results.csv b/summaries/jan_14_2026/jacs_set/p38/dg_results.csv new file mode 100644 index 0000000..7e8e6a5 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/p38/dg_results.csv @@ -0,0 +1,35 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2aa,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CO)CO)nc21,-8.949012784971796,0.07587086816724911,-9.27 +2y,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCC(C)(C)O)nc21,-9.722761801288462,0.0702721180324584,-9.78 +2z,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(C)(C)CO)nc21,-9.691950583667426,0.0702488771524907,-10.36 +3flw,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CCO)CCO)nc21,-11.59507847993429,0.0624297177091484,-10.68 +2bb,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCCS(C)(=O)=O)nc21,-10.13477654263652,0.07412826643705356,-9.06 +2v,CNc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-9.14123671654411,0.06535239933213995,-8.97 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a/summaries/jan_14_2026/jacs_set/ptp1b/README.md b/summaries/jan_14_2026/jacs_set/ptp1b/README.md new file mode 100644 index 0000000..df1ce51 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/ptp1b/README.md @@ -0,0 +1,39 @@ +# Ptp1B Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.41 +- RMSE: 2.07 +- R²: 0.37 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.73 + +## System Details +- Ligands: 23 +- Host Atoms: 4819 +- Map Details: + - Edges: 40 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 30 + - Mean Dummy Atoms: 11.2 + - Median Dummy Atoms: 11.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 11.25 Hours +- Average Time Per Edge: 0.28 Hours +- Total Nanoseconds Simulated: 5140.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/ptp1b/ddg_results.csv b/summaries/jan_14_2026/jacs_set/ptp1b/ddg_results.csv new file mode 100644 index 0000000..e91d5e2 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/ptp1b/ddg_results.csv @@ -0,0 +1,41 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +20667,23482,-18.967416701892066,0.05630604116153605,-20.712926898931823,0.05686495799798807,1.7455101970397564,0.08002495685345627,1.4099999999999995 +20667,23485,5.545661578518689,0.0461837755550426,3.663883895075734,0.04390758396763106,1.8817776834429545,0.06372454044081544,0.4100000000000002 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+23484,23486,1.787127816000603,0.04569202610182563,-0.6265643495591114,0.045261165234140255,2.4136921655597146,0.06431433998450159,-4.72 +23486,23485,5.006362170110385,0.0421704100897888,2.381209927072618,0.0396506900449624,2.6251522430377663,0.05788368257274792,1.4600000000000002 diff --git a/summaries/jan_14_2026/jacs_set/ptp1b/dg_comparison_plot.png b/summaries/jan_14_2026/jacs_set/ptp1b/dg_comparison_plot.png new file mode 100644 index 0000000..2f3f6cc Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/ptp1b/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/ptp1b/dg_plot.png b/summaries/jan_14_2026/jacs_set/ptp1b/dg_plot.png new file mode 100644 index 0000000..61ad551 Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/ptp1b/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/ptp1b/dg_results.csv b/summaries/jan_14_2026/jacs_set/ptp1b/dg_results.csv new file mode 100644 index 0000000..691e6d1 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/ptp1b/dg_results.csv @@ -0,0 +1,24 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +20667,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Br,-12.75865462117678,0.06421385759781074,-11.42 +23482,CS(=O)(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-11.254267708552574,0.05497813234537721,-10.01 +23485,Cc1c(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc(C(=O)[O-])c1OCC(=O)[O-],-10.853483159746464,0.06619315157616854,-11.01 +23486,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Cl,-13.344121571708932,0.06380427094943579,-12.47 +20669,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCc3ccccc3)c2)c1Br,-7.414781876450364,0.07033246530351686,-8.61 +23466,Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-4.9989991692919835,0.06727752445180374,-7.85 +23330,CC1(C)CC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC(C)(C)C1,-8.873508349955179,0.06825444623946994,-10.13 +20670,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCC3)c2)c1Br,-8.213552845237786,0.0533798090820362,-9.08 +23475,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCC3)c2)c1Br,-7.647724283043574,0.05470960149488422,-8.72 +23472,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NS(=O)(=O)c3ccc(F)cc3)c2)c1Br,-7.347175296204489,0.06909242019484015,-8.65 +23467,COc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-5.469140148127945,0.06015043204279213,-7.34 +23473,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(OCc3ccccc3)c2)c1Br,-8.09364546489706,0.06858502521300225,-8.39 +23468,CCC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.001812584161193,0.04858655264241835,-7.75 +23469,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC(=O)c3ccccc3)c2)c1Br,-7.135095895668855,0.08312413000190291,-7.72 +23471,COC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-6.6565251661796125,0.06073999699461835,-7.75 +23474,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCC3CCCCC3)c2)c1Br,-7.850330163594286,0.08384256473591856,-9.11 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b/summaries/jan_14_2026/jacs_set/thrombin/README.md @@ -0,0 +1,39 @@ +# Thrombin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.60 +- RMSE: 0.82 +- R²: 0.73 +- Kendall 𝜏: 0.75 +- Spearman ρ: 0.87 + +## System Details +- Ligands: 11 +- Host Atoms: 4784 +- Map Details: + - Edges: 19 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 6 + - Mean Dummy Atoms: 2.9 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 2.61 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 1182.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/thrombin/ddg_results.csv b/summaries/jan_14_2026/jacs_set/thrombin/ddg_results.csv new file mode 100644 index 0000000..bfaedb8 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/thrombin/ddg_results.csv @@ -0,0 +1,20 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +1a,3b,2.0834899930303683,0.042114491143104595,2.261101264525177,0.04035020957118013,-0.17761127149480865,0.0583246926839807,-0.37999999999999984 +1a,5,1.2440197547746976,0.038416009337613535,0.8263158713914662,0.040273271265346286,0.41770388338323144,0.05565722012317698,-0.0999999999999996 +1b,1c,0.11997456081161327,0.030948241692603067,0.06180994583594545,0.03071690369724693,0.05816461497566782,0.04360414930496542,-0.0999999999999996 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a/summaries/jan_14_2026/jacs_set/thrombin/dg_results.csv b/summaries/jan_14_2026/jacs_set/thrombin/dg_results.csv new file mode 100644 index 0000000..92196f3 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/thrombin/dg_results.csv @@ -0,0 +1,12 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(F)c1,-7.400904768431713,0.02946881713995741,-7.48 +3b,CCc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-7.726787649492081,0.033915897509054486,-7.86 +5,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1ccccc1,-6.990447323688992,0.03515215193308521,-7.58 +1b,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(Cl)c1,-8.437061353829119,0.02494869036054674,-8.46 +1c,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(Br)c1,-8.321558625540582,0.03410841272732401,-8.56 +1d,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cccc(I)c1,-6.661233982380119,0.0399960768217475,-8.25 +3a,Cc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-7.800870945403792,0.03070007633436919,-8.32 +6a,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1Cl,-10.695045632088869,0.031228198216033703,-9.18 +6b,Cc1ccc(Cl)cc1CNC(=O)[C@@H]1CCCN1C(=O)[C@H]([NH3+])Cc1ccccc1,-9.369677546433161,0.036755302771038625,-8.89 +7a,Cc1ccc(C)c(CNC(=O)[C@@H]2CCCN2C(=O)[C@H]([NH3+])Cc2ccccc2)c1,-8.091587661436417,0.040252763557009255,-8.22 +6e,[NH3+][C@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)NCc1cc(Cl)ccc1F,-10.214824511275154,0.040927415465792816,-8.91 diff --git a/summaries/jan_14_2026/jacs_set/tyk2/README.md b/summaries/jan_14_2026/jacs_set/tyk2/README.md new file mode 100644 index 0000000..7a88812 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/tyk2/README.md @@ -0,0 +1,39 @@ +# Tyk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.49 +- RMSE: 0.58 +- R²: 0.79 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.81 + +## System Details +- Ligands: 16 +- Host Atoms: 4670 +- Map Details: + - Edges: 28 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 13 + - Mean Dummy Atoms: 6.6 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 5.52 Hours +- Average Time Per Edge: 0.20 Hours +- Total Nanoseconds Simulated: 2594.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/jacs_set/tyk2/ddg_results.csv b/summaries/jan_14_2026/jacs_set/tyk2/ddg_results.csv new file mode 100644 index 0000000..661261f --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/tyk2/ddg_results.csv @@ -0,0 +1,29 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +ejm_31,ejm_45,18.14635195995238,0.04885115468050912,17.342131032442076,0.04656906219778326,0.8042209275103057,0.06749157627141356,-0.02000000000000026 +ejm_31,ejm_55,0.33217931088189045,0.04628744238581828,0.5969226470469062,0.045135337171246674,-0.2647433361650158,0.06465080033675197,0.3299999999999992 +ejm_42,ejm_46,24.578965075390457,0.056376173734823995,25.576068667289476,0.05657468284945156,-0.9971035918990201,0.07986843997784786,-1.5300000000000011 +ejm_42,ejm_48,24.22117608960247,0.06548887965056795,23.93742494962109,0.0644944855553675,0.2837511399813815,0.09191480851820386,0.7799999999999999 +ejm_42,ejm_54,-11.281101104242833,0.055061479545147694,-11.563483484221498,0.05505663598948582,0.2823823799786664,0.07786526630134558,-0.7499999999999996 +ejm_43,ejm_48,21.211914935902527,0.06026537376221223,22.06155645715983,0.05789844837167355,-0.8496415212573037,0.08357120077243407,-0.7399999999999994 +ejm_43,ejm_50,-14.276609875107342,0.052844152276761064,-12.896716069859474,0.050096231338666766,-1.3798938052478682,0.07281577318264723,-0.7200000000000009 +ejm_44,ejm_42,-8.137710575736495,0.05060519843796035,-5.396389566386605,0.04864875968828387,-2.7413210093498894,0.07019678004120801,-2.359999999999999 +ejm_44,ejm_43,-4.6294787771991786,0.05159162445057449,-2.7657517851386273,0.04962892012931238,-1.863726992060551,0.07158718758724066,-0.8399999999999999 +ejm_44,ejm_55,-17.2430199207561,0.05746008367184468,-13.452879864232127,0.054257822638547115,-3.790140056523972,0.0790289347837324,-1.7900000000000003 +ejm_45,ejm_50,-20.383277487583133,0.050559837626673355,-19.21046390658165,0.04930366282744548,-1.1728135810014801,0.07061974475341867,0.5799999999999991 +ejm_47,ejm_45,-28.009807925208325,0.06843563022715896,-28.170303686339587,0.06875653412654238,0.1604957611312596,0.09700977512438021,0.14000000000000012 +ejm_47,ejm_48,-34.66977563598716,0.06911160003111526,-35.18661499723241,0.07074274144641896,0.5168393612452524,0.09889867909237075,0.7000000000000006 +ejm_47,ejm_50,-68.62354386723904,0.0650839820009517,-68.00238144829252,0.06221372520258251,-0.621162418946514,0.09003595013483588,0.7199999999999991 +ejm_49,ejm_31,-15.938883047181335,0.051454470736961626,-14.24623751240502,0.04886799848842937,-1.6926455347763136,0.0709622705040219,-1.7899999999999994 +ejm_49,ejm_50,-29.626132640087704,0.0666186117455822,-27.96639024671438,0.06476439996617962,-1.659742393373323,0.09291107002875335,-1.2300000000000006 +ejm_49,ejm_55,-28.214237462972285,0.06725064454503582,-25.54611455379975,0.06448524845045497,-2.6681229091725336,0.09317186517098207,-1.4600000000000002 +ejm_50,ejm_46,36.497834406462076,0.058520177204040694,37.41140163077068,0.057977222894029894,-0.9135672243086054,0.08237699627017452,-2.3299999999999996 +ejm_50,ejm_54,-0.7524106108885967,0.05823391988668169,-0.7585790899899815,0.058054630666399085,0.0061684791013848035,0.08222852040004408,-1.549999999999998 +ejm_50,jmc_27,35.52501098216475,0.06179179132872944,36.331542837037645,0.06041573804639463,-0.806531854872899,0.08641925062914986,-2.2999999999999994 +ejm_55,ejm_54,-1.552807966084077,0.05202602382829196,-1.8588478136700135,0.05050576576467228,0.30603984758593644,0.0725088927708729,-1.3199999999999985 +jmc_23,ejm_46,2.8608004870044352,0.03321345892385583,2.2750593387418885,0.031528547633308576,0.5857411482625469,0.0457950124964768,0.38999999999999824 +jmc_23,jmc_28,7.804279064287304,0.033628065493892224,6.880540011833244,0.03409027993543741,0.9237390524540597,0.04788521666378875,0.7199999999999974 +jmc_23,jmc_30,-2.6267946608540425,0.034819801872321296,-3.175310600160381,0.03551241731206386,0.5485159393063384,0.04973480055025739,0.7599999999999997 +jmc_27,ejm_46,1.5111223331115904,0.034422930157800014,1.0886658222350265,0.03308889595008058,0.4224565108765639,0.04774738899504387,-0.030000000000000387 +jmc_27,jmc_30,-3.2994126072613192,0.04112516656176588,-3.801342883228328,0.04106371309077508,0.5019302759670087,0.05811633038599804,0.340000000000001 +jmc_28,jmc_27,-7.2089073351888375,0.035725378365524016,-6.3382094477009945,0.03463524651503881,-0.8706978874878438,0.04975844612241584,-0.29999999999999877 +jmc_28,jmc_30,-10.68596383577239,0.033480894408497865,-9.915964253196035,0.030881683605505358,-0.7699995825763533,0.045548311414403964,0.040000000000002214 diff --git a/summaries/jan_14_2026/jacs_set/tyk2/dg_comparison_plot.png b/summaries/jan_14_2026/jacs_set/tyk2/dg_comparison_plot.png new file mode 100644 index 0000000..01a0635 Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/tyk2/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/tyk2/dg_plot.png b/summaries/jan_14_2026/jacs_set/tyk2/dg_plot.png new file mode 100644 index 0000000..2d56656 Binary files /dev/null and b/summaries/jan_14_2026/jacs_set/tyk2/dg_plot.png differ diff --git a/summaries/jan_14_2026/jacs_set/tyk2/dg_results.csv b/summaries/jan_14_2026/jacs_set/tyk2/dg_results.csv new file mode 100644 index 0000000..f8fdf86 --- /dev/null +++ b/summaries/jan_14_2026/jacs_set/tyk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +ejm_31,CC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.983829519600977,0.05009716666110879,-9.54 +ejm_45,O=C(CC1CC1)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.102787420041622,0.05275067354230783,-9.56 +ejm_55,COC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.415944198318444,0.04705674693619667,-9.21 +ejm_42,CCC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.780986360273207,0.0417984647551433,-9.78 +ejm_46,O=C(Nc1ccnc(NC(=O)C2CC2)c1)c1c(Cl)cccc1Cl,-10.748392510214575,0.04569139869766123,-11.31 +ejm_48,O=C(Nc1ccnc(NC(=O)C2CCCC2)c1)c1c(Cl)cccc1Cl,-9.351959820816216,0.055464721656700314,-9.0 +ejm_54,CCNC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.892506856977976,0.04213287993963118,-10.53 +ejm_43,CC(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-8.635221070699352,0.04497065706452396,-8.26 +ejm_50,O=C(CO)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.05837354316189,0.029741886804056927,-8.98 +ejm_44,CC(C)(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-6.827202338155057,0.04734809127358964,-7.42 +ejm_47,O=C(Nc1ccnc(NC(=O)C2CCC2)c1)c1c(Cl)cccc1Cl,-9.514484717170953,0.05604218561558224,-9.7 +ejm_49,O=C(Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1)c1ccccc1,-8.174463837102211,0.057152278952521014,-7.75 +jmc_27,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2Cl)c1)c1c(Cl)cccc1Cl,-11.145699833088532,0.04224181014646968,-11.28 +jmc_23,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2F)c1)c1c(Cl)cccc1Cl,-11.278417815159692,0.049871784629246414,-11.7 +jmc_28,C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.21670639244338,0.04806405993053325,-10.98 +jmc_30,N#C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.81302376677591,0.05429814133736469,-10.94 diff --git a/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/README.md b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/README.md new file mode 100644 index 0000000..b9d2c29 --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/README.md @@ -0,0 +1,39 @@ +# Bace Ciordia Prospective Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.99 +- RMSE: 1.36 +- R²: 0.39 +- Kendall 𝜏: 0.50 +- Spearman ρ: 0.73 + +## System Details +- Ligands: 9 +- Host Atoms: 6230 +- Map Details: + - Edges: 17 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 4.0 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.19 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 1317.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/ddg_results.csv b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/ddg_results.csv new file mode 100644 index 0000000..a36429a --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/ddg_results.csv @@ -0,0 +1,18 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +spiro10,spiro1,1.5445450114925248,0.044805201638301685,-2.924937671838661,0.04165171403654024,4.469482683331186,0.06117492440559772,0.98 +spiro10,spiro15,7.185298698123247,0.05462761623365707,3.7682325879082224,0.05254211903297733,3.4170661102150244,0.07579479354050166,-0.5500000000000004 +spiro10,spiro6,0.2632806771663148,0.048613319994112635,-1.9036477386194903,0.046223977099011465,2.1669284157858053,0.0670813755054257,-1.0299999999999998 +spiro16,spiro1,-7.889434660779381,0.04698754784500042,-8.55435337988651,0.048770013000585956,0.6649187191071302,0.06772255031053931,0.6599999999999993 +spiro16,spiro15,-1.245580757703845,0.039964287234287334,-2.1433561282232,0.03867226298898164,0.8977753705193549,0.05561194277161678,-0.8700000000000011 +spiro16,spiro3,-0.5198936649024669,0.05037432551326554,-0.8021858356237305,0.05036980157512167,0.28229217072126356,0.07123685550074178,-0.8000000000000018 +spiro2,spiro1,16.444795166794695,0.04432582102783453,18.354265685204098,0.04464013444558209,-1.9094705184094043,0.06290882301483046,-0.48999999999999955 +spiro2,spiro15,22.749659295130076,0.049203215104937977,25.09590540406846,0.04805837441407072,-2.346246108938383,0.0687790936839517,-2.02 +spiro2,spiro3,24.636314304421166,0.04815408663442878,27.131597664922303,0.048527832134955574,-2.4952833605011366,0.06836495119075636,-1.9500000000000006 +spiro3,spiro15,-1.424116374141486,0.04505293527610464,-1.4132062494012598,0.04545281438855059,-0.010910124740226164,0.06399785397052705,-0.0699999999999992 +spiro4,spiro1,-10.956116632472487,0.05490653025880574,-10.645081363088424,0.05414764300873262,-0.3110352693840611,0.07711481251006387,0.10000000000000045 +spiro4,spiro15,-4.560964825622713,0.05909930664128539,-3.961882980620605,0.057833873044516176,-0.5990818450021081,0.08268908583851858,-1.43 +spiro5,spiro1,-10.16590921516117,0.05231423459954712,-9.104635397162795,0.053641743931409726,-1.061273817998374,0.0749280710664527,0.24000000000000057 +spiro5,spiro15,-3.5671201162707087,0.056965441669687804,-2.412956760191497,0.05659116685497116,-1.1541633560792113,0.08029708407302093,-1.2899999999999998 +spiro5,spiro4,1.5300873695997323,0.03839396139234073,1.4293562228916306,0.03810416858937406,0.10073114670810186,0.05409273458870416,0.14000000000000012 +spiro6,spiro1,0.45736032956417455,0.03519272765898311,-1.6537531262653398,0.03584412468298256,2.1111134558295146,0.05023275180963665,2.01 +spiro6,spiro15,7.0970043013547475,0.04685863941096037,4.939596166704265,0.04637456141699485,2.157408134650482,0.06592671714915764,0.4799999999999994 diff --git a/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_comparison_plot.png b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_comparison_plot.png new file mode 100644 index 0000000..fafb958 Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_plot.png b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_plot.png new file mode 100644 index 0000000..02c0d5f Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_results.csv b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_results.csv new file mode 100644 index 0000000..6f3e0c5 --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/bace_ciordia_prospective/dg_results.csv @@ -0,0 +1,10 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +spiro10,COCC#Cc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-11.943520042730329,0.03835342859137159,-8.5 +spiro1,N#Cc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-7.721085142281481,0.023171706605696826,-7.52 +spiro15,N#Cc1cc(Cl)cc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-7.986812807583144,0.020654159232032055,-9.05 +spiro6,CC#Cc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-9.902233873466024,0.03469432459279678,-9.53 +spiro16,N#Cc1cc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)cc(C(F)(F)F)c1,-8.619363194649498,0.03366751843108496,-8.18 +spiro3,NC1=[NH+][C@@]2(COc3ccc(-c4cc(Cl)cc(Cl)c4)cc32)[C@H](C(F)(F)F)C1,-8.16007915759699,0.03384599283739086,-8.98 +spiro2,NC1=[NH+][C@@]2(COc3ccc(-c4cncnc4)cc32)[C@H](C(F)(F)F)C1,-5.711956895794375,0.03592449746719544,-7.03 +spiro4,COc1cccc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-7.134214788298403,0.038446904143487726,-7.62 +spiro5,COc1cncc(-c2ccc3c(c2)[C@@]2(CO3)[NH+]=C(N)C[C@H]2C(F)(F)F)c1,-6.990734097599749,0.04153525731865121,-7.760000000000001 diff --git a/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/README.md b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/README.md new file mode 100644 index 0000000..22918d9 --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/README.md @@ -0,0 +1,39 @@ +# Bace P3 Arg368 In Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.22 +- RMSE: 1.49 +- R²: 0.59 +- Kendall 𝜏: 0.51 +- Spearman ρ: 0.72 + +## System Details +- Ligands: 21 +- Host Atoms: 6036 +- Map Details: + - Edges: 32 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 6.9 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 10.00 Hours +- Average Time Per Edge: 0.31 Hours +- Total Nanoseconds Simulated: 4256.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/ddg_results.csv b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/ddg_results.csv new file mode 100644 index 0000000..3b94465 --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/ddg_results.csv @@ -0,0 +1,33 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +17a,17b,16.49458684284608,0.06945149346566934,17.035845505479998,0.0680991555564441,-0.5412586626339189,0.09726769726950812,-0.6411999999999991 +17a,27a,16.36986030738639,0.06851649425859611,15.872515924549777,0.06702846982371956,0.4973443828366118,0.09585053861297554,1.7872 +17b,17d,11.54980493503224,0.052928214938469,12.223145416583028,0.05033010463227638,-0.6733404815507879,0.0730377667297451,0.1909999999999979 +17b,27b,20.01377100260475,0.07399070825306209,19.210831173216782,0.07479172865166925,0.8029398293879677,0.10520659476712795,1.6098599999999987 +17c,17d,13.16217353345517,0.05579996898564976,13.129070815024651,0.05571701479391363,0.03310271843052047,0.07885443726477709,0.35469999999999796 +17c,17e,17.05795051409735,0.06153562483686797,17.715373666697776,0.06141235474182665,-0.6574231526004243,0.08693739379001258,-0.20459999999999923 +17c,27c,19.938861020525042,0.07500087973756148,19.447350037118568,0.07240887429901181,0.4915109834064744,0.10425054934463536,1.7325999999999993 +17d,17g,-5.796210939795281,0.05295268250888099,-2.6754181197295197,0.05038088317138793,-3.1207928200657618,0.07309049167994008,0.2729000000000014 +17e,17f,-0.3019159063863364,0.0552558541822334,0.5169393105838912,0.052084219841255455,-0.8188552169702276,0.07593401989806986,0.31379999999999886 +17e,27e,18.29842854128093,0.07524970984929118,19.36447135620226,0.07366385928735178,-1.0660428149213281,0.10530376535295058,2.5920599999999996 +17f,27f,19.779658970200632,0.07323194557694211,19.09710003087932,0.07390723898543819,0.6825589393213095,0.1040442109270616,2.537470000000001 +17g,27f,33.20341899925034,0.08370177667796873,30.553968399277075,0.08321654494734794,2.649450599973259,0.11802957583598497,2.019070000000001 +17g,27g,20.593388782835614,0.07481646700292731,19.42949339257078,0.07380366460063058,1.163895390264834,0.10509274305718012,-1.1322999999999994 +27a,27b,12.2743808338967,0.06884817761933175,12.904889317930875,0.06759188973526892,-0.6305084840341737,0.09648178646505155,-0.8185400000000003 +27a,27d,22.714088322441153,0.07119140279261588,25.29988989580256,0.06851930192148857,-2.5858015733614086,0.09880845392671916,-0.12278000000000025 +27b,27c,-3.9354943776631037,0.06425814495946851,-3.271301385356236,0.0629299242161101,-0.6641929923068677,0.0899404500515615,-0.040959999999999594 +27c,27e,17.995710854457787,0.0620658172922789,17.847254772862225,0.059518811805816384,0.148456081595563,0.08599217775434423,0.6548600000000009 +27d,27e,5.075976169020254,0.07296285820221218,5.409057815084326,0.07186896888481711,-0.3330816460640722,0.10241448806493607,-0.08185999999999871 +27d,27g,-5.414274966937412,0.05277771961806433,-2.7189901729364028,0.05028126396626766,-2.6952847940010094,0.07289508347020736,-2.974019999999999 +27f,27g,-13.13096815990015,0.0619281215142829,-11.656400484406117,0.06127648177862528,-1.4745676754940324,0.08712002900283025,-3.1513700000000004 +8a,17a,-12.536896061091188,0.07053426970523664,-9.630309874504427,0.06892934637589267,-2.9065861865867624,0.09862219828547147,-3.1514499999999996 +8a,8b,17.42955543925293,0.06898640663016428,17.739449313563096,0.06968372760920959,-0.3098938743101678,0.09805583202062432,-0.7230499999999991 +8a,8c,13.054049638648932,0.06711945906490091,14.536282395278148,0.06888823097419414,-1.4822327566292157,0.09618009228483215,-0.5184100000000001 +8b,8c,-4.9257132410731606,0.04552270823849678,-3.3233163454963175,0.04543561017630232,-1.602396895576843,0.0643172732433536,0.20463999999999896 +8b,8d,10.105908774471281,0.05175568983861211,11.514051262598064,0.051451965131637946,-1.4081424881267832,0.0729791487109702,0.16370999999999877 +8c,8e,18.44690575087061,0.06376569886453469,17.707698320344342,0.06022742459259601,0.7392074305262697,0.08771206886591697,-0.10914000000000088 +8d,8e,5.66610153724355,0.051869921110163135,5.556996888271204,0.0485232882593831,0.10910464897234652,0.07102815089440054,-0.06821000000000067 +8d,8g,-6.033033774493009,0.05179438275225591,-2.693150262374441,0.05190194307795572,-3.339883512118568,0.07332441462401551,-2.005409999999999 +8e,8f,-0.3922253263217354,0.05084842018470386,0.04098289078213016,0.04982577285490456,-0.43320821710386553,0.0711910772208761,0.9549700000000011 +8f,17f,-11.878356038177092,0.07928290732543294,-7.03394433443962,0.07652699969132977,-4.844411703737472,0.11019147460547923,-4.174569999999999 +8f,8g,-13.997363453330593,0.06164186509986617,-11.879176323373688,0.060918722282848746,-2.1181871299569033,0.08666493095575022,-2.8921699999999997 +8g,17g,-11.261783973077343,0.0801972379247424,-6.629647757571862,0.07745465466794468,-4.63213621550548,0.11149358950400827,-0.764 diff --git a/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_comparison_plot.png b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_comparison_plot.png new file mode 100644 index 0000000..2d0cd59 Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_plot.png b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_plot.png new file mode 100644 index 0000000..0a11da9 Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_results.csv b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_results.csv new file mode 100644 index 0000000..e43e29c --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/bace_p3_arg368_in/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17a,Cc1nc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)co1,-9.373586463813615,0.060042846037666325,-10.9413 +17b,CN1C(=O)C[C@@](C)(c2cc(NC(=O)c3ccc(Cl)cn3)ccc2F)[NH+]=C1N,-10.323155230659191,0.06713479492720567,-11.5825 +27a,Cc1nc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)co1,-8.818181166511724,0.06832729619485897,-9.1541 +17d,COc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)cn1,-11.111210240675309,0.056311885716818326,-11.3915 +27b,CN1C(=O)CC[C@@](C)(c2cc(NC(=O)c3ccc(Cl)cn3)ccc2F)[NH+]=C1N,-9.75987953158105,0.06888662310138068,-9.97264 +17c,CN1C(=O)C[C@@](C)(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)[NH+]=C1N,-11.015640874662655,0.05901937968698083,-11.7462 +17e,CN1C(=O)C[C@@](C)(c2cc(NC(=O)c3cnc(OCC(F)(F)F)cn3)ccc2F)[NH+]=C1N,-11.276371946786883,0.06671648383287085,-11.9508 +27c,CN1C(=O)CC[C@@](C)(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)[NH+]=C1N,-10.869653212565634,0.06409004699368943,-10.0136 +17g,CC#CCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)cn1,-14.457432021385662,0.058745214114637595,-11.1186 +17f,COCCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CC(=O)N(C)C(N)=[NH+]3)c2)cn1,-12.30155438169093,0.07459559673294072,-11.637 +27e,CN1C(=O)CC[C@@](C)(c2cc(NC(=O)c3cnc(OCC(F)(F)F)cn3)ccc2F)[NH+]=C1N,-11.3636080213774,0.06937470969844454,-9.35874 +27f,COCCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)cn1,-11.842492306857018,0.06336973723775526,-9.09953 +27g,CC#CCOc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)cn1,-13.49256320347247,0.06385621905879017,-12.2509 +27d,COc1cnc(C(=O)Nc2ccc(F)c([C@]3(C)CCC(=O)N(C)C(N)=[NH+]3)c2)cn1,-11.015903457002153,0.07106945378465478,-9.27688 +8a,Cc1nc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)co1,-6.10870644718217,0.07445139321975959,-7.78985 +8b,CN1C(=O)[C@@](C)(c2cc(NC(=O)c3ccc(Cl)cn3)ccc2F)[NH+]=C1N,-6.000256621989218,0.06775604516923371,-8.5129 +8c,CN1C(=O)[C@@](C)(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)[NH+]=C1N,-7.652661528183513,0.0750431880761203,-8.30826 +8d,COc1cnc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)cn1,-7.11228361895818,0.0719473779793904,-8.34919 +8e,CN1C(=O)[C@@](C)(c2cc(NC(=O)c3cnc(OCC(F)(F)F)cn3)ccc2F)[NH+]=C1N,-7.057790686026237,0.07518268126885715,-8.4174 +8g,CC#CCOc1cnc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)cn1,-10.095043282380288,0.064139216925252,-10.3546 +8f,COCCOc1cnc(C(=O)Nc2ccc(F)c([C@@]3(C)[NH+]=C(N)N(C)C3=O)c2)cn1,-7.640945756238684,0.07181465768641178,-7.46243 diff --git a/summaries/jan_14_2026/janssen_bace/ciordia_retro/README.md b/summaries/jan_14_2026/janssen_bace/ciordia_retro/README.md new file mode 100644 index 0000000..113289f --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/ciordia_retro/README.md @@ -0,0 +1,39 @@ +# Ciordia Retro Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.78 +- RMSE: 0.99 +- R²: 0.32 +- Kendall 𝜏: 0.41 +- Spearman ρ: 0.55 + +## System Details +- Ligands: 32 +- Host Atoms: 6230 +- Map Details: + - Edges: 55 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 12.29 Hours +- Average Time Per Edge: 0.22 Hours +- Total Nanoseconds Simulated: 5093.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/janssen_bace/ciordia_retro/ddg_results.csv b/summaries/jan_14_2026/janssen_bace/ciordia_retro/ddg_results.csv new file mode 100644 index 0000000..b6d8841 --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/ciordia_retro/ddg_results.csv @@ -0,0 +1,56 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +11,15,4.32503225659783,0.05046023874693118,5.659433287561227,0.04959721417109478,-1.334401030963397,0.07075393521162437,0.7859300000000005 +11,16,1.140277218062115,0.049338356009828825,1.8450213725438487,0.04846748696685152,-0.7047441544817337,0.06916191630250375,1.64563 +11,22,9.322701988809397,0.05854144295484606,9.709855907755115,0.05915752968935818,-0.3871539189457173,0.08322688184825135,1.0964500000000004 +11,27,-1.2620185797787415,0.03828516883649815,-0.9296586692107047,0.040833748321223974,-0.3323599105680369,0.05597454023750647,-0.9090099999999998 +11,32,-13.479215441624847,0.03809140242482012,-13.516926377789536,0.037525598635320734,0.03771093616468987,0.05347079101368127,0.9818499999999998 +12,24,3.645439912964801,0.04175648982190353,3.1154507858312397,0.03719616664304497,0.5299891271335616,0.05592100906800506,0.6710599999999994 +12,26,5.263843708288271,0.05449801549227702,3.795074038393788,0.049353897659920584,1.4687696698944832,0.07352442387956794,0.09180000000000006 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b/summaries/jan_14_2026/janssen_bace/ciordia_retro/dg_plot.png new file mode 100644 index 0000000..4215aa2 Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/ciordia_retro/dg_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/ciordia_retro/dg_results.csv b/summaries/jan_14_2026/janssen_bace/ciordia_retro/dg_results.csv new file mode 100644 index 0000000..7054fb6 --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/ciordia_retro/dg_results.csv @@ -0,0 +1,33 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccccc4)cc32)[NH+]=C1N,-8.543398309803806,0.047565532142170165,-8.70337 +15,COc1ccccc1-c1ccc2c(c1)[C@@]1(CC(C)(C)O2)[NH+]=C(N)N(C)C1=O,-9.762524369317502,0.05588098107472974,-7.91744 +16,COc1ccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)cc1,-9.624961262555354,0.06022309928019801,-7.05774 +22,CC(C)Oc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-8.811818967632288,0.056964409308867044,-7.60692 +27,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(F)c4)cc32)[NH+]=C1N,-8.94299473814616,0.03844354467903084,-9.61238 +32,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccccn4)cc32)[NH+]=C1N,-8.333944303484722,0.05613795899848405,-7.721520000000001 +12,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(Cl)c4)cc32)[NH+]=C1N,-9.77830351560246,0.04996371669743564,-10.4569 +24,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(C(F)(F)F)c4)cc32)[NH+]=C1N,-9.129808793771508,0.045643574666807366,-9.78584 +26,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(OC(F)F)c4)cc32)[NH+]=C1N,-8.45645190705484,0.05013469096036257,-10.3651 +40,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccns4)cc32)[NH+]=C1N,-7.904944306386365,0.05111945268791413,-8.64597 +13,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccc(C#N)c4)cc32)[NH+]=C1N,-10.069834466988558,0.040399707393770815,-9.64326 +14,COc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-8.584148337546093,0.04958365275264195,-9.83624 +21,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cc(Cl)ccc4F)cc32)[NH+]=C1N,-9.900581877054286,0.05003468990334226,-10.2153 +35,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncc(C(F)(F)F)c4)cc32)[NH+]=C1N,-9.227268125023825,0.04211116598755562,-9.88176 +36,CC#Cc1cncc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-11.699504018367941,0.05514377236616781,-10.9787 +18,COc1cc(F)cc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-9.244772048856175,0.0616306331470552,-9.90099 +19,COc1ccc(F)c(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-9.056115224729473,0.06762013851574668,-9.91084 +23,CCOc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-8.876185184783665,0.06350909514939611,-9.81896 +37,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccnc4F)cc32)[NH+]=C1N,-9.047022200401726,0.05676880801982914,-9.45002 +31,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cccnc4)cc32)[NH+]=C1N,-8.717773890167978,0.055967135725503596,-9.53354 +33,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4ccncc4)cc32)[NH+]=C1N,-8.956091509272225,0.05971896604282774,-7.13992 +17,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cc(Cl)cc(Cl)c4)cc32)[NH+]=C1N,-10.81339585273813,0.055475160735931395,-10.3651 +20,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cc(F)cc(Cl)c4)cc32)[NH+]=C1N,-10.071678112829288,0.04941885821995009,-10.1676 +38,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncc(F)c4)cc32)[NH+]=C1N,-9.296380694911456,0.04582726482498986,-9.38493 +25,CSc1cccc(-c2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)c1,-8.5649311962055,0.06669596757486784,-8.87004 +1a,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(Br)cc32)[NH+]=C1N,-6.962294355968432,0.04568109174304317,-6.08468 +28,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(C4CCCCC4)cc32)[NH+]=C1N,-9.230847017582784,0.06066327350616936,-8.997 +29,CC(C)COc1ccc2c(c1)[C@@]1(CC(C)(C)O2)[NH+]=C(N)N(C)C1=O,-8.677191196594501,0.062019223659688,-8.73567 +30,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(N4CCCCC4)cc32)[NH+]=C1N,-8.54697325118063,0.05857624973431243,-6.94738 +39,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncnc4)cc32)[NH+]=C1N,-8.40567865678691,0.042018374191404924,-9.36077 +41,Cc1ccc(C(=O)Nc2ccc3c(c2)[C@@]2(CC(C)(C)O3)[NH+]=C(N)N(C)C2=O)o1,-9.310927901395038,0.06597390556816093,-9.10997 +34,CN1C(=O)[C@]2(CC(C)(C)Oc3ccc(-c4cncc(Cl)c4)cc32)[NH+]=C1N,-9.90650440686042,0.03623744116030914,-10.2494 diff --git a/summaries/jan_14_2026/janssen_bace/keranen_p2/README.md b/summaries/jan_14_2026/janssen_bace/keranen_p2/README.md new file mode 100644 index 0000000..4e88d8f --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/keranen_p2/README.md @@ -0,0 +1,39 @@ +# Keranen P2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.59 +- RMSE: 0.66 +- R²: 0.00 +- Kendall 𝜏: 0.02 +- Spearman ρ: 0.02 + +## System Details +- Ligands: 12 +- Host Atoms: 6003 +- Map Details: + - Edges: 19 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 8.6 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.49 Hours +- Average Time Per Edge: 0.24 Hours +- Total Nanoseconds Simulated: 1767.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/janssen_bace/keranen_p2/ddg_results.csv b/summaries/jan_14_2026/janssen_bace/keranen_p2/ddg_results.csv new file mode 100644 index 0000000..da5aaaf --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/keranen_p2/ddg_results.csv @@ -0,0 +1,20 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +29,31,5.956709513182233,0.05143524930230565,5.862274152018132,0.0501956133488124,0.09443536116410085,0.07186921782135802,-0.3699999999999997 +29,32,8.62136565178201,0.056951483194963896,8.803787983713578,0.05513590902764004,-0.18242233193156807,0.07926815187961968,-0.3699999999999997 +29,34,14.578777385752115,0.0552104980240728,14.264658704859508,0.05325196895184554,0.31411868089260714,0.07670704849826036,-0.16000000000000036 +29,35,30.780602111494527,0.06801248209774155,29.731066856603114,0.06629435472391908,1.049535254891412,0.0949770455918504,0.18000000000000063 +29,36 out,-1.9470120584909119,0.05286268364894196,-3.955335249831156,0.049678290872419074,2.008323191340244,0.07254237317990632,-0.3699999999999997 +30,31,2.3197290411027827,0.04279976830755327,2.4509239257919315,0.04221054852426328,-0.1311948846891492,0.06011281538823004,0.0 +30,32,4.564681915986413,0.05799427224631915,5.1705020994598545,0.057146475400125504,-0.6058201834734414,0.08141901045847545,0.0 +30,34,24.918932225081498,0.06446683537404393,25.016801678450896,0.062318368017201795,-0.09786945336939668,0.08966354808656349,0.20999999999999933 +31,32,2.779816971257473,0.04078194784214439,3.350530692287862,0.04094358270614764,-0.5707137210303892,0.05778878986978822,0.0 +33,35,22.06557943834087,0.07062754677507994,21.8589481635455,0.0714289999154762,0.20663127479536983,0.10045074610171498,0.4300000000000005 +33,37 out,-14.339547218534188,0.0555141697369976,-13.764150825285599,0.05462112861190748,-0.575396393248589,0.0778799764536862,-0.32000000000000073 +33,39 out,-13.284759212847135,0.06137542616306858,-12.490518500042517,0.05887663936102445,-0.7942407128046177,0.08504940681243119,0.5600000000000005 +34,39 out,-20.054693778427055,0.06146145663037017,-19.714208399261068,0.061448211471685825,-0.3404853791659902,0.08691026029299358,0.470000000000001 +35,38 out,-31.349044303441488,0.06905427993469156,-30.05045209113921,0.06768272334727041,-1.2985922123022766,0.0966925261693058,-0.6800000000000003 +36 out,28 out,-1.7455588438153495,0.03558131593193818,-1.8409707481777444,0.03777289455279296,0.09541190436239493,0.051892404129552656,-0.12999999999999998 +36 out,38 out,0.888760478678561,0.041380385003179615,1.1441366231422139,0.04085204851476714,-0.2553761444636529,0.05814831150484304,-0.12999999999999998 +37 out,28 out,0.9427535108079509,0.036840780309211986,0.4018634601517996,0.03679933887038505,0.5408900506561514,0.052071435884648444,0.07000000000000091 +37 out,38 out,2.6216796773065463,0.041553443962349924,3.4118139251621997,0.03922668394572173,-0.7901342478556534,0.0571438661494801,0.07000000000000091 +39 out,28 out,2.0690548139467104,0.03395942485693594,1.3913404294146485,0.03500295463188067,0.6777143845320617,0.048769348668762987,-0.8100000000000003 diff --git a/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_comparison_plot.png b/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_comparison_plot.png new file mode 100644 index 0000000..4f61fcf Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_plot.png b/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_plot.png new file mode 100644 index 0000000..781b895 Binary files /dev/null and b/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_plot.png differ diff --git a/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_results.csv b/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_results.csv new file mode 100644 index 0000000..466ba4e --- /dev/null +++ b/summaries/jan_14_2026/janssen_bace/keranen_p2/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +29,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1OC,-11.027646380298762,0.034888280233215815,-9.99 +31,CCCOc1cc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)ccc1OC,-10.761219491972001,0.051526151239330846,-10.36 +32,CCCCOc1cc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)ccc1OC,-11.26458138603522,0.049328345066859236,-10.36 +34,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1OC1CCCC1,-10.482492312277795,0.048062058112177064,-10.15 +35,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C1CCCC1,-9.452639667866283,0.0544226036359171,-9.81 +36 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1F,-9.662072063575566,0.037601308192421946,-10.36 +30,CCOc1cc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)ccc1OC,-10.58257772510366,0.053303234975122536,-10.36 +33,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1OC(C)C,-9.479541100544944,0.049983641972904086,-10.24 +37 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1Cl,-9.89103564986039,0.03978595664939367,-10.56 +39 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C#N,-10.34040772108068,0.04512973944487058,-9.68 +38 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C(F)(F)F,-10.37313956747269,0.03933794499966333,-10.49 +28 out,COc1ccc([C@]2(c3cccc(-c4cccnc4)c3)[NH+]=C(N)N(C)C2=O)cc1C,-9.532646933912007,0.03627088436889106,-10.49 diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/README.md b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/README.md new file mode 100644 index 0000000..4b60ddf --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/README.md @@ -0,0 +1,39 @@ +# Hne Map Charge -1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.38 +- RMSE: 0.38 +- R²: 1.00 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 2 +- Host Atoms: 3804 +- Map Details: + - Edges: 1 + - Min Dummy Atoms: 10 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 10.0 + - Median Dummy Atoms: 10.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 0.65 Hours +- Average Time Per Edge: 0.65 Hours +- Total Nanoseconds Simulated: 96.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/ddg_results.csv b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/ddg_results.csv new file mode 100644 index 0000000..1973a10 --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/ddg_results.csv @@ -0,0 +1,2 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +16,19,-7.85359173240555,0.051277919142003116,-8.92264336001468,0.053737495274054935,1.0690516276091295,0.07427747565623703,0.3025999999999995 diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_comparison_plot.png b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_comparison_plot.png new file mode 100644 index 0000000..bc20b81 Binary files /dev/null and b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_plot.png b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_plot.png new file mode 100644 index 0000000..424c6e1 Binary files /dev/null and b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_plot.png differ diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_results.csv b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_results.csv new file mode 100644 index 0000000..2763834 --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/hne_negative_1/dg_results.csv @@ -0,0 +1,3 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +16,CCOC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N(CC(=O)[O-])[C@@H]1c1ccc(C#N)cc1,-12.221825813804564,0.040395342209561286,-11.8386 +19,CC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N(CC(=O)[O-])[C@@H]1c1ccc(C#N)cc1,-11.152774186195435,0.04039534220956114,-11.536 diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_neutral/README.md b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/README.md new file mode 100644 index 0000000..dead4d2 --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/README.md @@ -0,0 +1,39 @@ +# Hne Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.77 +- RMSE: 0.98 +- R²: 0.71 +- Kendall 𝜏: 0.76 +- Spearman ρ: 0.89 + +## System Details +- Ligands: 14 +- Host Atoms: 3804 +- Map Details: + - Edges: 24 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 25 + - Mean Dummy Atoms: 8.2 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 6.14 Hours +- Average Time Per Edge: 0.26 Hours +- Total Nanoseconds Simulated: 2828.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_neutral/ddg_results.csv b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/ddg_results.csv new file mode 100644 index 0000000..eb419fe --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/ddg_results.csv @@ -0,0 +1,25 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +14,15,-14.743625988967691,0.056742659602737854,-14.798152611254629,0.06183373354120322,0.05452662228693754,0.08392341760460366,-1.9527000000000008 +14,17,-4.703466103630561,0.040386015758849564,-4.462771506830406,0.03876767896083221,-0.2406945968001541,0.05598181133979319,-1.0885000000000007 +14,22,-9.456557900293147,0.06549220662302445,-8.562549737494704,0.06593710838099057,-0.894008162798444,0.09293509234944261,-1.0358000000000007 +15,17,10.34455368543995,0.06979369547490276,9.901063950835358,0.0669036923155157,0.443489734604593,0.0966812493376697,0.8642000000000001 +15,23,-8.551412175771194,0.06658884846542344,-7.857831666850927,0.06563536212852021,-0.6935805089202678,0.09349906684931733,1.9070999999999996 +18,20,-3.9211313057906403,0.03760479107388129,-3.18296382126463,0.03771084377127969,-0.7381674845260101,0.05325624892585025,0.2552000000000012 +18,22,-3.9209648835591757,0.056331911864329946,-2.569622569414598,0.058796803952981834,-1.351342314144578,0.08142695161539586,-0.6028000000000004 +18,25,5.197013383879438,0.06252644205710285,7.5406083758671425,0.06422807399147343,-2.343594991987705,0.08963705397308874,-1.2413000000000003 +20,22,-0.17904571469242553,0.06184177039283399,0.13986839413087768,0.06155142882964283,-0.3189141088233032,0.0872524094583673,-0.8580000000000017 +20,25,8.577278834912184,0.06511422554212298,10.603338989666407,0.06701224383535588,-2.0260601547542234,0.09343716172808147,-1.4965000000000015 +22,23,-14.689253845299472,0.05712512780173301,-13.536750585616852,0.06185516800524379,-1.1525032596826195,0.08419823059495529,0.9901999999999996 +22,26,1.5682517039766957,0.04977157388616543,3.489375017754403,0.048711410609029226,-1.9211233137777073,0.06964202101193982,-1.2195999999999996 +23,25,23.046512548562273,0.05195093930323716,23.224197120903593,0.052649088824204035,-0.17768457234131915,0.0739650366626527,-1.6286999999999996 +25,27,2.09834870040644,0.04747828306517435,4.155423226176067,0.050841684005568065,-2.0570745257696266,0.06956338257545314,-2.4881999999999995 +25,29,-26.733306535737995,0.054093175466525985,-24.59706034709781,0.056625574928982514,-2.1362461886401882,0.07831045503692455,-1.8978999999999995 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b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/dg_plot.png differ diff --git a/summaries/jan_14_2026/mcs_docking_set/hne_neutral/dg_results.csv b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/dg_results.csv new file mode 100644 index 0000000..588ebf6 --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/hne_neutral/dg_results.csv @@ -0,0 +1,15 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +14,CCOC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N[C@@H]1c1ccc(C#N)cc1,-10.126741957311168,0.04852650429995568,-10.3255 +15,CCOC(=O)C1=C(C)N(c2cccc(C(F)(F)F)c2)C(=O)N(CC(N)=O)[C@@H]1c1ccc(C#N)cc1,-10.591955893896971,0.06226444972857124,-12.2782 +17,CC1=C(C(=O)OCCO)[C@@H](c2ccc(C#N)cc2)NC(=O)N1c1cccc(C(F)(F)F)c1,-10.33678396836968,0.05920198841259017,-11.414 +22,CC1=C(C#N)[C@@H](c2ccc(C#N)cc2)NC(=O)N1c1cccc(C(F)(F)F)c1,-10.848316856040004,0.035445609296348275,-11.3613 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+30,CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[S@](C)(=N)=O)N(C)C(=O)N1c1cccc(C(F)(F)F)c1,-13.847161617053121,0.056114827139460886,-13.0996 +6,CCOC(=O)C1=C(N)N(c2cccc([N+](=O)[O-])c2)C2=CCCC(O)=C2[C@@H]1c1ccc(Br)cc1,-9.093703404632196,0.08477010203748965,-7.03256 diff --git a/summaries/jan_14_2026/mcs_docking_set/renin/README.md b/summaries/jan_14_2026/mcs_docking_set/renin/README.md new file mode 100644 index 0000000..1f2818d --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/renin/README.md @@ -0,0 +1,39 @@ +# Renin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.25 +- RMSE: 1.64 +- R²: 0.28 +- Kendall 𝜏: 0.41 +- Spearman ρ: 0.54 + +## System Details +- Ligands: 29 +- Host Atoms: 5321 +- Map Details: + - Edges: 56 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 24 + - Mean Dummy Atoms: 9.6 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 14.19 Hours +- Average Time Per Edge: 0.25 Hours +- Total Nanoseconds Simulated: 6059.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/mcs_docking_set/renin/ddg_results.csv b/summaries/jan_14_2026/mcs_docking_set/renin/ddg_results.csv new file mode 100644 index 0000000..52693a9 --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/renin/ddg_results.csv @@ -0,0 +1,57 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err 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file mode 100644 index 0000000..c65dee2 --- /dev/null +++ b/summaries/jan_14_2026/mcs_docking_set/renin/dg_results.csv @@ -0,0 +1,30 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +b1a2m,O=C(c1c(Cc2ccccc2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-9.597482410965824,0.04623527038124311,-9.60566 +b1i2a,O=C(c1c(Oc2ccccc2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-9.689715707712729,0.043627187944099415,-8.69953 +b1i2c,O=C(c1c(Oc2cccc(C(F)(F)F)c2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-6.812235436623262,0.06332796685699925,-6.88372 +b1i2h,O=C(c1c(Oc2cccc(F)c2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-10.420331775990219,0.04395967366505797,-9.82353 +b1i1,O=C(c1c(N2CCCCC2)n(-c2ccccc2)c2ccccc12)N1CC[NH2+]CC1,-6.728197561438384,0.0812139214228655,-7.39449 +b1i2e,Cc1ccccc1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-11.235782463962192,0.04706751681706276,-10.4744 +b1i2j,Cc1ccc(F)cc1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-12.262199888049798,0.055329073933274284,-11.3246 +b1i2k,Cc1cccc(F)c1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-10.320635838637108,0.05881350531631446,-10.6355 +b1i2d,COc1ccccc1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-9.745795472076006,0.05444845592809419,-8.41399 +b1i2g,Cc1cccc(Oc2c(C(=O)N3CC[NH2+]CC3)c3ccccc3n2-c2ccccc2)c1,-9.367002838940078,0.0491525541888863,-8.338 +b1i4b,O=C(c1c(Oc2ccccc2)n(-c2ccc(F)cc2)c2ccccc12)N1CC[NH2+]CC1,-9.919283852129197,0.04617568843692714,-8.39094 +b1i4a,O=C(c1c(Oc2ccccc2)n(-c2ccccn2)c2ccccc12)N1CC[NH2+]CC1,-8.27767690232689,0.05073492447365199,-7.23542 +b1i5a,COc1ccc2c(C(=O)N3CC[NH2+]CC3)c(Oc3cc(F)ccc3C)n(-c3ccccc3)c2c1,-13.786111531433246,0.06187710484707605,-10.3953 +b1i2i,Cc1cccc(C)c1Oc1c(C(=O)N2CC[NH2+]CC2)c2ccccc2n1-c1ccccc1,-10.141012756621457,0.05855812809954354,-9.81412 +b1i5b,COc1ccc2c(c1)c(C(=O)N1CC[NH2+]CC1)c(Oc1cc(F)ccc1C)n2-c1ccccc1,-12.27823410831274,0.06831883282293476,-8.00772 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+b1i5o,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccc(S(C)(=O)=O)cc2n1-c1ccccc1,-6.236905113060974,0.0671564585382538,-10.0361 +b1i5c,Cc1ccc(F)cc1Oc1c(C(=O)N2CC[NH2+]CC2)c2cc(O)ccc2n1-c1ccccc1,-13.83847451671485,0.06329618054008553,-11.8676 +b1i5i,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2ccc(O)cc2n1-c1ccccc1,-10.563630324937384,0.05586984381677019,-11.4568 +b1i5j,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2cc(O)ccc2n1-c1ccccc1,-11.259912734993112,0.05698278370228665,-11.4568 +b1i5l,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2cccc(F)c2n1-c1ccccc1,-8.490929685585721,0.06055636055068319,-9.653 +b1i5k_xray,Cc1c(F)cccc1Cc1c(C(=O)N2CC[NH2+]CC2)c2c(C)c(O)ccc2n1-c1ccccc1,-9.354851243597787,0.05916314974654154,-11.8676 diff --git a/summaries/jan_14_2026/merck/cdk8/README.md b/summaries/jan_14_2026/merck/cdk8/README.md new file mode 100644 index 0000000..59b0832 --- /dev/null +++ b/summaries/jan_14_2026/merck/cdk8/README.md @@ -0,0 +1,39 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.43 +- RMSE: 1.64 +- R²: 0.71 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.84 + +## System Details +- Ligands: 32 +- Host Atoms: 10498 +- Map Details: + - Edges: 57 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 20 + - Mean Dummy Atoms: 10.7 + - Median Dummy Atoms: 10.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 27.35 Hours +- Average Time Per Edge: 0.48 Hours +- Total Nanoseconds Simulated: 8014.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/cdk8/ddg_results.csv b/summaries/jan_14_2026/merck/cdk8/ddg_results.csv new file mode 100644 index 0000000..e4fdde3 --- /dev/null +++ b/summaries/jan_14_2026/merck/cdk8/ddg_results.csv @@ -0,0 +1,58 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +13,42-flipped,17.769379185442585,0.07191678910716585,21.44172213994119,0.07134007013469461,-3.6723429544986077,0.10129871747612462,-0.24159999999999987 +14,16-flipped,4.935578367547626,0.07217121077622055,7.44151508321001,0.06968345591132483,-2.505936715662384,0.10032182062069649,-0.9521699999999991 +14,17-flipped,-0.8975282142556025,0.07547099281191559,-0.5164772770802482,0.0735335017790231,-0.3810509371753544,0.10537099524965021,-0.6547699999999993 +14,18-flipped,-6.10012162099135,0.07672271210544238,-0.7393523241400919,0.07181740334407369,-5.360769296851259,0.10509097951727331,-2.6407399999999996 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(kcal/mol) +13,Cc1cccc(Cc2n[nH]c3cc(O)c(C(=O)N4CC[C@H](O)C4)cc23)c1,-8.780983827963052,0.07884553576210189,-11.2832 +42-flipped,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CC[C@H](O)C5)cc34)ccc21,-12.62808512584921,0.0736304441540466,-11.5248 +14,CNC(=O)c1ccc2[nH]nc(CC(C)C)c2c1,-5.952546867093634,0.114842544483918,-8.33796 +16-flipped,CNC(=O)c1ccc2[nH]nc(Cc3cccc(C)c3)c2c1,-8.67567194708355,0.10393132670661022,-9.29013 +17-flipped,CNC(=O)c1ccc2[nH]nc(Cc3ccc4cnn(C)c4c3)c2c1,-7.604654746456661,0.09604100874925074,-8.99273 +18-flipped,CNC(=O)c1ccc2[nH]nc(Cc3ccc4c(cnn4C)c3)c2c1,-9.810676858911496,0.07482814511285009,-10.9787 +15,CNC(=O)c1ccc2[nH]nc(Cc3ccc(OC)c(OC)c3)c2c1,-7.893637576575944,0.06652213955719628,-7.687929999999999 +44-flipped,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CC(O)C5)cc34)ccc21,-13.383923466900715,0.08192477907934657,-11.5248 +45-flipped,COC1CN(C(=O)c2ccc3[nH]nc(Cc4ccc5c(cnn5C)c4)c3c2)C1,-12.3574388223013,0.08213258220050486,-11.1913 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+38,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCC(F)(F)C5)cc34)cc2)cn1,-12.664442118171566,0.06611617890737832,-11.3918 +40,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCNCC5)cc34)cc2)cn1,-12.969942791724236,0.08465667909948986,-11.1913 +41,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCCCC5)cc34)cc2)cn1,-12.229467842711195,0.08273761154566918,-11.2832 +39,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCOCC5)cc34)cc2)cn1,-13.157333013846658,0.0814850513408491,-11.5248 +43,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CCC(F)(F)C5)cc34)ccc21,-10.84406983661028,0.07941299486577681,-11.938 diff --git a/summaries/jan_14_2026/merck/cmet_positive_1/README.md b/summaries/jan_14_2026/merck/cmet_positive_1/README.md new file mode 100644 index 0000000..8656745 --- /dev/null +++ b/summaries/jan_14_2026/merck/cmet_positive_1/README.md @@ -0,0 +1,39 @@ +# Cmet Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.92 +- RMSE: 1.14 +- R²: 0.63 +- Kendall 𝜏: 0.68 +- Spearman ρ: 0.84 + +## System Details +- Ligands: 12 +- Host Atoms: 4581 +- Map Details: + - Edges: 20 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 52 + - Mean Dummy Atoms: 19.8 + - Median Dummy Atoms: 16.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.28 Hours +- Average Time Per Edge: 0.36 Hours +- Total Nanoseconds Simulated: 3146.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/cmet_positive_1/ddg_results.csv b/summaries/jan_14_2026/merck/cmet_positive_1/ddg_results.csv new file mode 100644 index 0000000..9e5fca8 --- /dev/null +++ b/summaries/jan_14_2026/merck/cmet_positive_1/ddg_results.csv @@ -0,0 +1,21 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +CHEMBL3402741_400,CHEMBL3402763_90,-7.609036712346115,0.06704342093184446,-7.958209857952995,0.06829971477633105,0.34917314560687923,0.09570617184263852,-0.8837800000000005 +CHEMBL3402742_23,CHEMBL3402741_400,17.70145675995096,0.07064490814877258,17.571767955551824,0.0699029433160258,0.12968880439913907,0.09938372367541895,1.6921300000000004 +CHEMBL3402741_400,CHEMBL3402764_90,-11.873830728363478,0.07663796919242535,-13.945209966388553,0.07836930935686662,2.071379238025077,0.10961353461599256,-0.8837800000000005 +CHEMBL3402743_42,CHEMBL3402763_90,8.665677129080176,0.0762743209627309,9.255519438909582,0.07728400743166415,-0.5898423098294046,0.10858448251487507,0.4515500000000008 +CHEMBL3402743_42,CHEMBL3402764_90,3.6666929236633345,0.05168908754645395,2.68945278681978,0.05052097007099505,0.9772401368435544,0.0722781446102441,0.4515500000000008 +CHEMBL3402756_2.7 redocked,CHEMBL3402757_6.5 redocked,3.160157366387096,0.04093737664044749,2.6373488339538462,0.03940273124331807,0.5228085324332501,0.056819398409654165,0.5204999999999994 +CHEMBL3402742_23,CHEMBL3402756_2.7 redocked,10.795736170158996,0.0925264695681371,12.569260307170426,0.0984283979226187,-1.7735241370114294,0.13508995924330117,-1.2691999999999994 +CHEMBL3402742_23,CHEMBL3402757_6.5 redocked,14.031990551729052,0.09647253404230755,15.443027895777876,0.10182027836630145,-1.4110373440488237,0.1402651735504409,-0.7487 +CHEMBL3402756_2.7 redocked,CHEMBL3402758_10 redocked,-7.713821498679242,0.046274162177519264,-8.045481921385274,0.045197770387015446,0.3316604227060323,0.06468490189517741,0.7757000000000005 +CHEMBL3402743_42,CHEMBL3402765_11-charged-pKa-8.1,18.952756544390727,0.06686560583410933,18.839741080521495,0.0643511165943473,0.11301546386922955,0.0928012685823947,-0.7937999999999983 +CHEMBL3402756_2.7 redocked,CHEMBL3402759_5.7 redocked,6.2023525358751295,0.049831370468016695,5.523856257629434,0.04694279953502178,0.6784962782456965,0.06846014834125008,0.4426999999999998 +CHEMBL3402760_1 redocked,CHEMBL3402758_10 redocked,-8.087802819713456,0.05078534717430114,-8.607057988960934,0.0480948087118633,0.5192551692474766,0.06994470753849084,1.3642000000000014 +CHEMBL3402760_1 redocked,CHEMBL3402759_5.7 redocked,3.667413817233472,0.05352399383646984,2.577073628992195,0.05353411286492448,1.0903401882412764,0.07570151356770176,1.0312000000000008 +CHEMBL3402762_1 redocked,CHEMBL3402757_6.5 redocked,-11.467958651187931,0.0787639368464619,-14.582272253801518,0.07981621979947463,3.1143136026135863,0.1121355728153715,1.1090000000000002 +CHEMBL3402763_90,CHEMBL3402764_90,-4.300581657940227,0.0741296441755298,-5.964653936212019,0.07346638606342379,1.6640722782717925,0.10436720762198579,0.0 +CHEMBL3402762_1 redocked,CHEMBL3402760_1 redocked,-15.782633288590572,0.07784951581419924,-16.24820370049742,0.07607053399610883,0.46557041190684634,0.10884518021005067,0.0 +CHEMBL3402762_1 redocked,CHEMBL3402759_5.7 redocked,-11.303585196941903,0.08221781919237107,-13.960661625595721,0.08337166531536784,2.657076428653819,0.11709228996909715,1.0312000000000008 +CHEMBL3402765_11-charged-pKa-8.1,CHEMBL3402742_23,-21.426408981483625,0.08497643263014439,-19.696069415375607,0.08395082996296743,-1.7303395661080183,0.11945181436050496,0.43699999999999906 +CHEMBL3402764_90,CHEMBL3402758_10 redocked,-2.238766270859759,0.09073322577804456,2.0014781671708053,0.0916025832475901,-4.240244438030564,0.1289323524865706,-1.3018499999999988 +CHEMBL3402765_11-charged-pKa-8.1,CHEMBL3402764_90,-15.092316473893463,0.07254688226460462,-16.206868341567517,0.07219874844939252,1.1145518676740551,0.10235091305881479,1.245349999999999 diff --git a/summaries/jan_14_2026/merck/cmet_positive_1/dg_comparison_plot.png b/summaries/jan_14_2026/merck/cmet_positive_1/dg_comparison_plot.png new file mode 100644 index 0000000..1460f9f Binary files /dev/null and b/summaries/jan_14_2026/merck/cmet_positive_1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/merck/cmet_positive_1/dg_plot.png b/summaries/jan_14_2026/merck/cmet_positive_1/dg_plot.png new file mode 100644 index 0000000..deea48e Binary files /dev/null and b/summaries/jan_14_2026/merck/cmet_positive_1/dg_plot.png differ diff --git a/summaries/jan_14_2026/merck/cmet_positive_1/dg_results.csv b/summaries/jan_14_2026/merck/cmet_positive_1/dg_results.csv new file mode 100644 index 0000000..e9c7247 --- /dev/null +++ b/summaries/jan_14_2026/merck/cmet_positive_1/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3402741_400,CC[NH+](CC)CCCOC(=O)Nc1cccc(CN2N=C(c3ccc(OC)c(OC)c3)CSC2=O)c1,-9.934840412394859,0.07135672745217585,-8.72837 +CHEMBL3402763_90,CC[NH+](CC)CCCOC(=O)Nc1cccc(CN2N=C(c3ccc(Cl)cc3)CSC2=O)c1,-9.489478741753553,0.07797646538965074,-9.61215 +CHEMBL3402742_23,C[NH+](C)CCCOC(=O)Nc1cccc(CN2N=C(c3cc(F)cc(F)c3)CSC2=O)c1,-10.229232924975106,0.05840438089337451,-10.4205 +CHEMBL3402764_90,C[NH+](C)CCCOC(=O)Nc1cccc(Cn2nc(-c3ccc(F)cc3)ccc2=O)c1,-7.7892802502482095,0.055256204000179804,-9.61215 +CHEMBL3402743_42,C[NH+](C)CCCOC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-8.814924599719365,0.0655726852655371,-10.0637 +CHEMBL3402756_2.7 redocked,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-12.15834131433568,0.05187523198904032,-11.6897 +CHEMBL3402757_6.5 redocked,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(F)c4)ccc3=O)c2)nc1,-11.495976132654764,0.055408776150358476,-11.1692 +CHEMBL3402758_10 redocked,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccnc4)ccc3=O)c2)nc1,-12.009720113693215,0.05767078238635277,-10.914 +CHEMBL3402765_11-charged-pKa-8.1,O=C(Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1)OCCC[NH+]1CCOCC1,-8.719829212499542,0.08115240533479189,-10.8575 +CHEMBL3402759_5.7 redocked,COc1cccc(-c2ccc(=O)n(Cc3cccc(-c4ncc(OCCC[NH+](C)C)cn4)c3)n2)c1,-11.517370835555413,0.0667189964663154,-11.247 +CHEMBL3402760_1 redocked,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(C#N)c4)ccc3=O)c2)nc1,-12.737163733174896,0.0700200308619793,-12.2782 +CHEMBL3402762_1 redocked,C[N@H+]1CC[C@H](COc2cnc(-c3cccc(Cn4nc(-c5cccc(C#N)c5)ccc4=O)c3)nc2)CC1,-13.974511728995397,0.07334252075596777,-12.2782 diff --git a/summaries/jan_14_2026/merck/eg5_neutral/README.md b/summaries/jan_14_2026/merck/eg5_neutral/README.md new file mode 100644 index 0000000..d9e83fc --- /dev/null +++ b/summaries/jan_14_2026/merck/eg5_neutral/README.md @@ -0,0 +1,39 @@ +# Eg5 Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.82 +- RMSE: 0.94 +- R²: 0.68 +- Kendall 𝜏: 0.48 +- Spearman ρ: 0.64 + +## System Details +- Ligands: 9 +- Host Atoms: 5474 +- Map Details: + - Edges: 15 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 27 + - Mean Dummy Atoms: 11.9 + - Median Dummy Atoms: 8.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.00 Hours +- Average Time Per Edge: 0.27 Hours +- Total Nanoseconds Simulated: 1673.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/eg5_neutral/ddg_results.csv b/summaries/jan_14_2026/merck/eg5_neutral/ddg_results.csv new file mode 100644 index 0000000..cc72d7e --- /dev/null +++ b/summaries/jan_14_2026/merck/eg5_neutral/ddg_results.csv @@ -0,0 +1,16 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +CHEMBL1078774,CHEMBL1078691,-0.6869067935422433,0.04382994863125922,-0.7935948841783292,0.04182113491336848,0.10668809063608604,0.06058111688027045,0.4131000000000003 +CHEMBL1078774,CHEMBL1089056,8.990216838701775,0.04864855208234796,7.230118147141106,0.049042098214064245,1.76009869156067,0.06907828180366711,1.1647799999999995 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+CHEMBL1085895,CHEMBL1088740,24.01892174631577,0.07187846362515435,19.608612160800032,0.07265711497790245,4.410309585515737,0.1022035708281505,2.1708300000000005 +CHEMBL1089393,CHEMBL1088740,2.291809004415727,0.034128623453683976,1.908607830375635,0.034158781548023244,0.3832011740400922,0.04828649185526861,-0.32123999999999975 +CHEMBL1085895,CHEMBL1093088,17.494752558683153,0.07035532728932463,15.93581224622119,0.06810821070848129,1.558940312461965,0.09792139931546563,-0.36129999999999907 +CHEMBL1089393,CHEMBL1078691,-2.323167154911924,0.05468723570744775,2.001745287030763,0.054424396251621564,-4.324912441942686,0.07715379871837463,-1.819569999999998 +CHEMBL1089056,CHEMBL1093088,-11.441960655360052,0.06982144479559223,-10.66386257410684,0.06612329367299788,-0.7780980812532128,0.09616300806188133,-1.7854800000000006 +CHEMBL1089393,CHEMBL1085895,-21.457940792484433,0.07383258453402126,-17.68856212922675,0.07209914210802562,-3.7693786632576844,0.10319659312054187,-2.49207 +CHEMBL1093088,CHEMBL1088740,6.135566483182084,0.06174453271306523,3.271873111061631,0.061702477958720414,2.863693372120453,0.08729022342852125,2.5321299999999995 diff --git a/summaries/jan_14_2026/merck/eg5_neutral/dg_comparison_plot.png b/summaries/jan_14_2026/merck/eg5_neutral/dg_comparison_plot.png new file mode 100644 index 0000000..84de8fd Binary files /dev/null and b/summaries/jan_14_2026/merck/eg5_neutral/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/merck/eg5_neutral/dg_plot.png b/summaries/jan_14_2026/merck/eg5_neutral/dg_plot.png new file mode 100644 index 0000000..1576875 Binary files /dev/null and b/summaries/jan_14_2026/merck/eg5_neutral/dg_plot.png differ diff --git a/summaries/jan_14_2026/merck/eg5_neutral/dg_results.csv b/summaries/jan_14_2026/merck/eg5_neutral/dg_results.csv new file mode 100644 index 0000000..17b5258 --- /dev/null +++ b/summaries/jan_14_2026/merck/eg5_neutral/dg_results.csv @@ -0,0 +1,10 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1078774,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)c(F)c1)N2,-11.53947340252119,0.03910552304268305,-10.6625 +CHEMBL1078691,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)cc1)N2,-11.419085841697626,0.0366110327297107,-10.2494 +CHEMBL1089056,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-9.603334919212822,0.03485898164786469,-9.49772 +CHEMBL1084115,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccsc1)N2,-10.412409499111554,0.0593487834717757,-9.49772 +CHEMBL1078998,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1cccs1)N2,-10.383653942664102,0.043129617075185984,-10.4326 +CHEMBL1088740,Cc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-7.205821390159295,0.034886252625696564,-8.75107 +CHEMBL1085895,O=C(NCCCO)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.531645342810513,0.056928789026045055,-10.9219 +CHEMBL1089393,Clc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-7.492230665706562,0.041962307699245034,-8.42983 +CHEMBL1093088,FC(F)(F)c1ccc2c(c1)[C@H]1O[C@@H](Cn3cncn3)CC[C@H]1[C@H](c1ccccc1)N2,-10.138284996116337,0.05060331145869506,-11.2832 diff --git a/summaries/jan_14_2026/merck/eg5_positive_1/README.md b/summaries/jan_14_2026/merck/eg5_positive_1/README.md new file mode 100644 index 0000000..d105164 --- /dev/null +++ b/summaries/jan_14_2026/merck/eg5_positive_1/README.md @@ -0,0 +1,39 @@ +# Eg5 Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.39 +- RMSE: 1.53 +- R²: 0.00 +- Kendall 𝜏: 0.05 +- Spearman ρ: 0.08 + +## System Details +- Ligands: 19 +- Host Atoms: 5474 +- Map Details: + - Edges: 31 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 36 + - Mean Dummy Atoms: 16.8 + - Median Dummy Atoms: 16.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 11.17 Hours +- Average Time Per Edge: 0.36 Hours +- Total Nanoseconds Simulated: 4724.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/eg5_positive_1/ddg_results.csv b/summaries/jan_14_2026/merck/eg5_positive_1/ddg_results.csv new file mode 100644 index 0000000..fdcbfbe --- /dev/null +++ b/summaries/jan_14_2026/merck/eg5_positive_1/ddg_results.csv @@ -0,0 +1,32 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) 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+mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1082248,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-9.958428493735823,0.05694697663195947,-11.6963 +CHEMBL1096002,OCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Cl)cc(F)c1N[C@H]2c1ccccc1,-10.203013989511453,0.05390122820369523,-11.1913 +CHEMBL1083517,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccc(O)cc1,-13.324993493405119,0.06275763895008794,-11.5248 +CHEMBL1077227,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1cccs1,-10.555034719677746,0.06321807657288904,-11.3918 +CHEMBL1086410,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-9.871545850091989,0.06646425317695032,-11.5248 +CHEMBL1077204,C[NH+](C)CCNC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.664613791733762,0.07415226358140499,-11.1117 +CHEMBL1084676,C[NH+](C)CCOC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.841887576975685,0.06980165647304788,-10.7782 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+## Statistics Summary +- MUE: 1.55 +- RMSE: 1.85 +- R²: 0.11 +- Kendall 𝜏: 0.17 +- Spearman ρ: 0.24 + +## System Details +- Ligands: 41 +- Host Atoms: 1758 +- Map Details: + - Edges: 70 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 4.6 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 13.12 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 7184.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/hif2a/ddg_results.csv 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b/summaries/jan_14_2026/merck/hif2a_jmc2023/README.md new file mode 100644 index 0000000..0ca4e8c --- /dev/null +++ b/summaries/jan_14_2026/merck/hif2a_jmc2023/README.md @@ -0,0 +1,39 @@ +# Hif2A Jmc2023 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.00 +- RMSE: 1.16 +- R²: 0.47 +- Kendall 𝜏: 0.49 +- Spearman ρ: 0.70 + +## System Details +- Ligands: 38 +- Host Atoms: 1937 +- Map Details: + - Edges: 62 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.8 + - Median Dummy Atoms: 5.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 19.92 Hours +- Average Time Per Edge: 0.32 Hours +- Total Nanoseconds Simulated: 10779.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/hif2a_jmc2023/ddg_results.csv b/summaries/jan_14_2026/merck/hif2a_jmc2023/ddg_results.csv new file mode 100644 index 0000000..5671217 --- /dev/null +++ b/summaries/jan_14_2026/merck/hif2a_jmc2023/ddg_results.csv @@ -0,0 +1,63 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +19a-bindingpose1,19b,-3.5438890475351497,0.04080099944827415,-3.4882341723820027,0.04039822809786407,-0.05565487515314673,0.05741723077112934,-0.07620975148280228 +19a-bindingpose1,19c-bindingpose2,-3.1670367034286544,0.051223103325562125,-3.8599741661050633,0.05047386047790822,0.6929374626764088,0.07191256431142307,-0.02433663464145134 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4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 19.28 Hours +- Average Time Per Edge: 0.27 Hours +- Total Nanoseconds Simulated: 6996.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/pfkfb3/ddg_results.csv b/summaries/jan_14_2026/merck/pfkfb3/ddg_results.csv new file mode 100644 index 0000000..e8f68ab --- /dev/null +++ b/summaries/jan_14_2026/merck/pfkfb3/ddg_results.csv @@ -0,0 +1,72 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err 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+52,CCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.999581340109216,0.06035743643871305,-10.3953 +53,CCCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.99315681414812,0.06234718287258481,-6.99764 +70,Cc1coc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-10.822811257738524,0.05628937096563693,-10.3039 +38,CN(C)c1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-9.257456916521406,0.06887487512642416,-8.75876 +69,Cc1csc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-10.657513402023893,0.04246070862247591,-10.7146 +41,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(OC(F)(F)F)c2)c2nccnc2c1,-8.651518815856164,0.09058441139395988,-7.38769 +43,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(Br)c2)c2nccnc2c1,-8.587767141809854,0.07932328728019922,-7.997660000000001 +44,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(Br)cc2)c2nccnc2c1,-7.594019869988838,0.06068920781667139,-9.94868 +46,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(C(F)(F)F)cc2)c2nccnc2c1,-6.353889799624192,0.062267325624662535,-7.859360000000001 +48,COc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.942690990779373,0.06259806662722027,-8.00636 +63,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nsnc3c2)c2nccnc2c1,-8.121056816051254,0.05873262378940708,-8.56164 +47,CCc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.0951077261221265,0.05879757431275022,-8.33345 +64,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ncsc3c2)c2nccnc2c1,-8.143910564803752,0.061065584296464796,-9.42228 +49,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(N)cc2)c2nccnc2c1,-6.467370058274706,0.06682281582251567,-7.93429 +62_flip,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nonc3c2)c2nccnc2c1,-7.8843727070506295,0.07705177695474134,-7.691739999999999 +54,CC(C)n1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.387761902618857,0.06523138598872952,-8.17959 +56,Cc1cc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc2c1ccn2C,-10.292707081371306,0.053062789956052014,-10.5657 +58,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)CCO3)c2nccnc2c1,-9.377215620172104,0.0720310509841732,-9.13315 +39,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(N)c2)c2nccnc2c1,-6.779546371759693,0.07003884186420192,-7.1975 +59,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)OCCO3)c2nccnc2c1,-9.01024964685776,0.07216024324889832,-8.11517 +65,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3scnc3c2)c2nccnc2c1,-9.221145551263572,0.04581050103221578,-9.4879 +67,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)nc3c2)c2nccnc2c1,-11.187642483301365,0.058437805009279635,-10.2436 +68,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)cc3c2)c2nccnc2c1,-9.64203928491431,0.05882136179606202,-9.77823 diff --git a/summaries/jan_14_2026/merck/shp2/README.md b/summaries/jan_14_2026/merck/shp2/README.md new file mode 100644 index 0000000..28e4170 --- /dev/null +++ b/summaries/jan_14_2026/merck/shp2/README.md @@ -0,0 +1,39 @@ +# Shp2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.69 +- RMSE: 2.27 +- R²: 0.27 +- Kendall 𝜏: 0.38 +- Spearman ρ: 0.52 + +## System Details +- Ligands: 26 +- Host Atoms: 8365 +- Map Details: + - Edges: 46 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 27 + - Mean Dummy Atoms: 7.8 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 13.96 Hours +- Average Time Per Edge: 0.30 Hours +- Total Nanoseconds Simulated: 5065.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/shp2/ddg_results.csv b/summaries/jan_14_2026/merck/shp2/ddg_results.csv new file mode 100644 index 0000000..bade71d --- /dev/null +++ b/summaries/jan_14_2026/merck/shp2/ddg_results.csv @@ -0,0 +1,47 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +11,Example 30,-35.43380699715812,0.05130043227020721,-36.188848565138535,0.05409625975381212,0.7550415679804141,0.07455293200446264,-2.80301 +10,Example 30,-39.721808968191,0.04957161071500312,-41.28713624788681,0.05356831067715578,1.5653272796958115,0.07298567323580768,-2.00282 +11,10,2.9223109869187156,0.053390545731524505,4.946238587235993,0.054516604925003424,-2.023927600317278,0.0763060324355743,-0.8001900000000003 +3,Example 27,62.50040353688492,0.052703618219540546,66.25973035937709,0.053933001761764514,-3.7593268224921648,0.07540848793382333,-3.0555899999999996 +10,Example 23,-7.840809815859099,0.054170548469958814,-10.426394490229043,0.055952151818918994,2.585584674369945,0.0778786980804348,-1.5860599999999994 +4,3,1.586920649172482,0.042777069468705,0.3509944044499846,0.041391021182398284,1.2359262447224975,0.05952389693939869,0.35913000000000034 +3,6,-11.543342435538898,0.07174180463278072,-11.578831337523399,0.07142270609631077,0.03548890198449901,0.10123284782168318,-2.5671000000000004 +4,SHP836-2,0.6593634487315234,0.052649903226857225,-0.1526246368599606,0.049907419343759425,0.811988085591484,0.07254490206314489,-0.8911400000000002 +4,Example 27,64.92041250237308,0.05946889220334024,66.45432102557547,0.05856787289303591,-1.533908523202389,0.08346702867065121,-2.6964599999999996 +7,6,-26.38440638071559,0.054863429951613696,-26.256172016637684,0.05336846919102838,-0.12823436407790342,0.07653881008906115,-0.9535700000000006 +Example 1,6,-5.842035652793447,0.05592972512114,-6.4205298989470085,0.05443667505304702,0.5784942461535614,0.07804797078052261,0.9581399999999994 +Example 14,6,-56.6605509417933,0.07984007756667788,-63.46635841570419,0.07793055789302193,6.805807473910893,0.11156885694211795,1.7481900000000012 +Example 14,Example 27,16.413114508360344,0.08097752881836362,10.26707844918771,0.07807975443701194,6.146036059172634,0.11248914714972727,1.259700000000002 +Example 14,Example 9,-1.5320520733556606,0.07874278288748818,0.6907392988910607,0.07760088844924275,-2.2227913722467214,0.11055461883149849,0.9841300000000008 +Example 1,7,20.609877462647482,0.06745425811201664,19.924851489234552,0.06455688088319057,0.6850259734129284,0.09336845188182687,1.91171 +Example 1,Example 3,-7.325083623162857,0.06700056396674034,-5.6743686020753215,0.06409414758041491,-1.650715021087535,0.09272073838101848,0.7723099999999985 +Example 1,Example 4,-7.827216238807338,0.06706792554866668,-5.5817954181348615,0.06420589017504254,-2.245420820672477,0.09284666375573826,0.7870899999999983 +Example 1,Example 5,4.530728072840831,0.05227929606749285,2.1361801092386012,0.04741180808882546,2.39454796360223,0.07057623072652852,1.4250899999999995 +Example 22,Example 24,0.030664052916555454,0.044930250751355774,-0.6050709628851855,0.04609463176498292,0.635735015801741,0.06436957752020032,0.1616100000000009 +Example 1,Example 8,57.15957541219778,0.06298463955698728,65.34241645320678,0.06226794562090642,-8.18284104100899,0.08856840222094879,-0.7241499999999998 +Example 22,Example 26,0.608890558607062,0.05306661220588256,-0.8200848345424199,0.05140064283760386,1.428975393149482,0.07387889695392345,0.27978000000000075 +Example 24,Example 23,1.056363681528992,0.03927587843936261,1.9174349977609335,0.04151928600880488,-0.8610713162319416,0.05715282790785185,0.3368800000000002 +Example 24,Example 25,2.7221973457361974,0.03798395584686491,1.3912226013283935,0.04012714420618584,1.330974744407804,0.05525367502637827,0.20730999999999877 +Example 25,Example 23,-0.7764067270776805,0.046989830742803725,0.5582826098094403,0.04793387322366989,-1.3346893368871209,0.06712451411712565,0.1295700000000014 +Example 22,Example 6,-73.57749630295928,0.061784523818000335,-73.91785918701963,0.05811793402792833,0.34036288406035875,0.0848234733967649,0.16957000000000022 +Example 26,Example 23,0.6535083602998957,0.0502017788338722,1.890885956779535,0.04942939578747467,-1.2373775964796394,0.07045199618179628,0.21871000000000032 +Example 2,Example 1,-1.9327235996028698,0.037326876719560594,-1.2200202338258344,0.03536951969784011,-0.7127033657770354,0.05142274447453358,-0.7119599999999986 +Example 26,Example 25,-1.3681407573720548,0.059023359369492594,-1.2986529390002042,0.060366544761071075,-0.06948781837185043,0.08442675332885109,0.08913999999999891 +Example 2,Example 30,33.07904261345945,0.047541034945492895,36.67858470428823,0.044658453804578294,-3.5995420908287747,0.06522673914817627,-0.8808799999999991 +Example 29,Example 30,-36.37756214251119,0.07160614548976227,-35.05585579155534,0.0693224875224405,-1.3217063509558475,0.09966467452512912,-1.5343200000000004 +Example 30,Example 23,30.62805214550306,0.04708591092417118,31.006340977621957,0.048166636106530686,-0.3782888321188973,0.06735805698933074,0.4167600000000003 +Example 29,Example 28,10.0587174232765,0.07902633064418223,11.281018510151348,0.07579716153255639,-1.222301086874849,0.10950055082727238,-0.8345700000000004 +Example 4,Example 3,-0.26992158342158695,0.03684449953942022,-0.2875204647035176,0.03590448246670742,0.017598881281930705,0.051445592692789886,-0.014779999999999875 +Example 2,Example 4,-8.771617223773568,0.07564832955434615,-6.262995987492603,0.0727752519714227,-2.5086212362809643,0.10497098200868193,0.07512999999999972 +Example 30,Example 3,-41.48189116154034,0.0696495043871289,-43.65268169575903,0.06565774293171099,2.170790534218688,0.0957182985027384,0.9412299999999989 +Example 30,Example 5,-30.854376055777102,0.05691984111993189,-35.95684076172194,0.0543662366070385,5.102464705944842,0.07871185422749728,1.5940100000000001 +Example 6,Example 5,11.777243861909188,0.048580406941898906,8.430317534783278,0.04279451066655442,3.3469263271259093,0.06474122397538017,1.5061700000000007 +Example 6,Example 28,94.55042186023854,0.07621566206441484,96.7610999336315,0.07386774312213093,-2.210678073392956,0.10613797914919147,0.6119100000000006 +Example 9,Example 8,5.276338368825184,0.051412375514960564,4.340895369277216,0.048570344472523515,0.9354429995479676,0.07072701547690892,-0.9182299999999988 +Example 9,7,-35.27579210064168,0.06365070718956524,-41.969702878233505,0.06327898809663764,6.6939107775918245,0.08975323314659021,1.717630000000001 +SHP099-1 Example 7,11,10.116296286124392,0.047127013421842244,9.525876586700733,0.048203117458353005,0.5904196994236586,0.06741287656498775,3.3985599999999994 +SHP836-2,3,0.3546530651167897,0.04258872273560058,0.46874816953150694,0.0423560915819681,-0.1140951044147173,0.06006527947450117,1.2502700000000004 +SHP099-1 Example 7,Example 8,-3.686126288084092,0.05527535971327828,0.7905334543889375,0.055488340307165,-4.4766597424730294,0.07832190818331777,0.04032000000000021 +SHP099-1 Example 7,Example 28,22.485843185815916,0.07207341256714177,21.726238432054412,0.07129726031390372,0.7596047537615047,0.10137986056087264,1.2952999999999997 +SHP099-1 Example 7,Example 29,10.991750484719311,0.06863687310518181,8.535233233692647,0.06649651309943046,2.4565172510266655,0.09556571877006712,2.12987 +SHP836-2,6,-13.108297202546485,0.06894597243482666,-11.237489392385449,0.06558588316135651,-1.870807810161035,0.09515805370560594,-1.31683 diff --git a/summaries/jan_14_2026/merck/shp2/dg_comparison_plot.png b/summaries/jan_14_2026/merck/shp2/dg_comparison_plot.png new file mode 100644 index 0000000..203a795 Binary files /dev/null and b/summaries/jan_14_2026/merck/shp2/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/merck/shp2/dg_plot.png b/summaries/jan_14_2026/merck/shp2/dg_plot.png new file mode 100644 index 0000000..964d2c2 Binary files /dev/null and b/summaries/jan_14_2026/merck/shp2/dg_plot.png differ diff --git a/summaries/jan_14_2026/merck/shp2/dg_results.csv b/summaries/jan_14_2026/merck/shp2/dg_results.csv new file mode 100644 index 0000000..49ef879 --- /dev/null +++ b/summaries/jan_14_2026/merck/shp2/dg_results.csv @@ -0,0 +1,27 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,CNc1nc(N2CCC(C)([NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-9.507496515781186,0.041650592524081854,-6.35409 +Example 30,CC1([NH3+])CCN(c2nnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.149357714914842,0.03473634612141403,-9.1571 +10,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)cn2)CC1,-11.231017623897989,0.05038057010099566,-7.15428 +3,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-4.658920744158451,0.08326071843013128,-5.46294 +Example 27,C[C@@H]1CN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-7.710598313869583,0.08130323208235522,-8.51853 +Example 23,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Cl)CC1,-8.920400190795105,0.054531507450563725,-8.74034 +4,C[C@@H]1CN(c2ncc(-c3ccc(Cl)c(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-5.813786427925467,0.080633563375278,-5.82207 +6,Nc1nc(N2CCC([NH3+])CC2)ncc1-c1cccc(Cl)c1Cl,-5.955891357857038,0.057049756525210674,-8.03004 +SHP836-2,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-4.607252844512552,0.08356832943894475,-6.71321 +7,C[NH+](C)C1CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-6.362937582848616,0.06372117992791168,-7.07647 +Example 1,CC1([NH3+])CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-6.330750124824704,0.04351185647603997,-8.98818 +Example 14,Nc1nc(N2CC[C@@H](C[NH3+])C2)cnc1-c1cccc(Cl)c1Cl,-12.941077800672932,0.07595004118922587,-9.77823 +Example 9,Nc1nc(N2CCC(C[NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-14.45566476352033,0.0643446396873742,-8.7941 +Example 3,CC1([NH3+])CCN(c2ncc(-c3ccc(Cl)s3)c(N)n2)CC1,-7.811966177054203,0.05452801816876348,-8.21587 +Example 4,Cc1ccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)s1,-8.018130557868679,0.06197089000194306,-8.20109 +Example 5,COc1cc(Cl)c(Cl)c(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1,-4.113071600099951,0.052988881626401606,-7.56309 +Example 22,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Br)CC1,-8.630752165493321,0.06175701538852081,-9.23883 +Example 24,Cc1nc(-c2cccc(Cl)c2Cl)c(N)nc1N1CCC(C)([NH3+])CC1,-8.229711313869327,0.06126761566071964,-9.07722 +Example 8,CC1(C[NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-14.098992997773012,0.05167805324276602,-9.71233 +Example 26,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C(N)=O)CC1,-7.375680364033382,0.06037469037868041,-8.95905 +Example 25,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C#N)CC1,-7.230910941782066,0.05571231815155271,-8.86991 +Example 6,CC1([NH3+])CCN(c2ncc(-c3cc(O)cc(Cl)c3Cl)c(N)n2)CC1,-7.653601629520962,0.06447859682392898,-9.06926 +Example 2,Cc1cccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1Cl,-5.581273247655664,0.05218794221105539,-8.27622 +Example 29,CC1([NH3+])CCN(c2cnc(C3=CCCCC3)c(N)n2)CC1,-7.820518829014024,0.0665521032202836,-7.62278 +Example 28,CC1([NH3+])CCN(c2cnc(-c3cccc4cc[nH]c34)c(N)n2)CC1,-9.387606547143369,0.0735631225992428,-8.45735 +SHP099-1 Example 7,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-10.007861623113222,0.053835993200065935,-9.75265 diff --git a/summaries/jan_14_2026/merck/syk_negative_1/README.md b/summaries/jan_14_2026/merck/syk_negative_1/README.md new file mode 100644 index 0000000..f9d22b8 --- /dev/null +++ b/summaries/jan_14_2026/merck/syk_negative_1/README.md @@ -0,0 +1,39 @@ +# Syk Map Charge -1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.73 +- RMSE: 0.88 +- R²: 0.63 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.09 + +## System Details +- Ligands: 6 +- Host Atoms: 4405 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 4 + - Max Dummy Atoms: 25 + - Mean Dummy Atoms: 13.3 + - Median Dummy Atoms: 11.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.13 Hours +- Average Time Per Edge: 0.46 Hours +- Total Nanoseconds Simulated: 1563.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/syk_negative_1/ddg_results.csv b/summaries/jan_14_2026/merck/syk_negative_1/ddg_results.csv new file mode 100644 index 0000000..b35feb6 --- /dev/null +++ b/summaries/jan_14_2026/merck/syk_negative_1/ddg_results.csv @@ -0,0 +1,10 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +CHEMBL3264995,CHEMBL3265001,18.723188812784397,0.06363125740534584,19.357468488507777,0.06263093454862459,-0.6342796757233808,0.08928365405503673,0.3435000000000003 +CHEMBL3264997,CHEMBL3264995,0.2147116318176976,0.06975987673978508,0.06675650287432384,0.06874706512970787,0.14795512894337373,0.09794181623136414,-1.3984999999999994 +CHEMBL3264997,CHEMBL3265001,10.299987986347567,0.07176475138639977,10.170518791262808,0.06962761525119358,0.12946919508475901,0.09999092132348823,-1.0549999999999993 +CHEMBL3265001,redocked CHEMBL3265000 ground state,-27.22917865533107,0.07296689044525953,-27.2977274963896,0.07186239840638131,0.06854884105853397,0.10241275021191446,0.22690000000000118 +docked CHEMBL3264994,CHEMBL3264995,-10.612298944666955,0.0764089182782446,-7.344984753504825,0.07445525529058407,-3.26731419116213,0.10668602454322454,-2.576540000000002 +docked CHEMBL3264994,redocked CHEMBL3265000 ground state,-18.084758906628704,0.08728589505485342,-15.12027700731992,0.0855834223680606,-2.964481899308784,0.12224299431769799,-2.0061400000000003 +docked CHEMBL3264998,CHEMBL3264997,0.7880828748394888,0.07116415165185479,0.8974746458769276,0.0714913114718647,-0.1093917710374388,0.1008729106167526,0.729099999999999 +docked CHEMBL3264998,redocked CHEMBL3265000 ground state,-13.027084488329368,0.07740542312396032,-14.223314733225441,0.07562091745711597,1.1962302448960733,0.10821332028015439,-0.09899999999999907 +docked CHEMBL3264998,docked CHEMBL3264994,11.807210002433935,0.08620677499517905,7.427590841532098,0.08553011201375696,4.379619160901838,0.12143725999937267,1.9071400000000012 diff --git a/summaries/jan_14_2026/merck/syk_negative_1/dg_comparison_plot.png b/summaries/jan_14_2026/merck/syk_negative_1/dg_comparison_plot.png new file mode 100644 index 0000000..7b0f2e0 Binary files /dev/null and b/summaries/jan_14_2026/merck/syk_negative_1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/merck/syk_negative_1/dg_plot.png b/summaries/jan_14_2026/merck/syk_negative_1/dg_plot.png new file mode 100644 index 0000000..7d47b16 Binary files /dev/null and b/summaries/jan_14_2026/merck/syk_negative_1/dg_plot.png differ diff --git a/summaries/jan_14_2026/merck/syk_negative_1/dg_results.csv b/summaries/jan_14_2026/merck/syk_negative_1/dg_results.csv new file mode 100644 index 0000000..7adcb93 --- /dev/null +++ b/summaries/jan_14_2026/merck/syk_negative_1/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3264995,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-11.743057119478518,0.04774539843662738,-12.3815 +CHEMBL3265001,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5nnn[n-]5)cc4)c3)cn3ccnc23)cc1OC,-12.097605352161198,0.051631008165706184,-12.038 +CHEMBL3264997,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4cccc(C(=O)[O-])c4)c3)cn3ccnc23)cc1OC,-12.254941172562063,0.04949384258991441,-10.983 +redocked CHEMBL3265000 ground state,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(/C([O-])=N/S(C)(=O)=O)cc4)c3)cn3ccnc23)cc1OC,-11.631774830480296,0.05403710265984264,-11.8111 +docked CHEMBL3264994,CC(C)(C)c1ccc(Nc2nc(-c3cccc(NC(=O)c4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1,-8.44333433285811,0.05318997001121753,-9.80496 +docked CHEMBL3264998,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(CC(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-12.559947192459813,0.05316684366028711,-11.7121 diff --git a/summaries/jan_14_2026/merck/syk_neutral/README.md b/summaries/jan_14_2026/merck/syk_neutral/README.md new file mode 100644 index 0000000..3dc36c9 --- /dev/null +++ b/summaries/jan_14_2026/merck/syk_neutral/README.md @@ -0,0 +1,39 @@ +# Syk Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.89 +- RMSE: 1.05 +- R²: 0.04 +- Kendall 𝜏: -0.06 +- Spearman ρ: -0.05 + +## System Details +- Ligands: 40 +- Host Atoms: 4405 +- Map Details: + - Edges: 67 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 42 + - Mean Dummy Atoms: 9.8 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 20.02 Hours +- Average Time Per Edge: 0.30 Hours +- Total Nanoseconds Simulated: 8198.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/syk_neutral/ddg_results.csv b/summaries/jan_14_2026/merck/syk_neutral/ddg_results.csv new file mode 100644 index 0000000..e88a46e --- /dev/null +++ b/summaries/jan_14_2026/merck/syk_neutral/ddg_results.csv @@ -0,0 +1,68 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +CHEMBL3259820,CHEMBL3265015 flip,7.554883037830312,0.06034827367679299,5.336433994581211,0.057021354943261215,2.2184490432491004,0.08302619499492005,1.0983799999999997 +CHEMBL3259820,intermediate_1,21.486481120982805,0.08804793849418827,21.31426862546654,0.08709855259879695,0.17221249551626508,0.12384909098528646, +CHEMBL3264996,CHEMBL3265003 tautomer 2,22.305205932164096,0.06958231880787182,23.226647388007127,0.06839267345794171,-0.9214414558430309,0.09756667911436237,-0.15509999999999968 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adjust,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(N)=O)cc4)c3)cn3ccnc23)cc1OC,-10.892373844378254,0.09321760446274494,-11.414 diff --git a/summaries/jan_14_2026/merck/tnks2_neutral/README.md b/summaries/jan_14_2026/merck/tnks2_neutral/README.md new file mode 100644 index 0000000..69bf9b8 --- /dev/null +++ b/summaries/jan_14_2026/merck/tnks2_neutral/README.md @@ -0,0 +1,39 @@ +# Tnks2 Map Charge 0 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.71 +- RMSE: 0.91 +- R²: 0.27 +- Kendall 𝜏: 0.30 +- Spearman ρ: 0.44 + +## System Details +- Ligands: 21 +- Host Atoms: 3286 +- Map Details: + - Edges: 33 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 14 + - Mean Dummy Atoms: 4.5 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.83 Hours +- Average Time Per Edge: 0.15 Hours +- Total Nanoseconds Simulated: 2474.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/tnks2_neutral/ddg_results.csv b/summaries/jan_14_2026/merck/tnks2_neutral/ddg_results.csv new file mode 100644 index 0000000..67f29b6 --- /dev/null +++ b/summaries/jan_14_2026/merck/tnks2_neutral/ddg_results.csv @@ -0,0 +1,34 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +1a,1b,-0.03282304853388433,0.048491259832441055,1.7197588740834235,0.047760821981512644,-1.7525819226173078,0.06806245952422711,-1.3866100000000006 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+5p,5o_adjust,-5.097807783997181,0.058691943961049674,-4.714911621563155,0.05487424214771149,-0.3828961624340268,0.08034878180291641,-1.5347000000000013 diff --git a/summaries/jan_14_2026/merck/tnks2_neutral/dg_comparison_plot.png b/summaries/jan_14_2026/merck/tnks2_neutral/dg_comparison_plot.png new file mode 100644 index 0000000..d41014a Binary files /dev/null and b/summaries/jan_14_2026/merck/tnks2_neutral/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/merck/tnks2_neutral/dg_plot.png b/summaries/jan_14_2026/merck/tnks2_neutral/dg_plot.png new file mode 100644 index 0000000..c102991 Binary files /dev/null and b/summaries/jan_14_2026/merck/tnks2_neutral/dg_plot.png differ diff --git a/summaries/jan_14_2026/merck/tnks2_neutral/dg_results.csv b/summaries/jan_14_2026/merck/tnks2_neutral/dg_results.csv new file mode 100644 index 0000000..d56c2c2 --- /dev/null +++ b/summaries/jan_14_2026/merck/tnks2_neutral/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1a,O=c1[nH]c(-c2ccccc2)nc2ccccc12,-8.354398280993532,0.054000811574565634,-8.55056 +1b,COc1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-9.889051660466384,0.05335980614019308,-9.93717 +3a,CC(C)(C)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-11.072051502850652,0.0540741593575046,-10.9965 +5a,CC(C)(O)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-10.876125290058347,0.049279936457619446,-10.7585 +5b,CC(C)(O)c1ccc(-c2nc3cccc(F)c3c(=O)[nH]2)cc1,-11.261278436884563,0.05071086622838386,-10.4744 +3b,CC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.279625260939747,0.04892183815439644,-11.5193 +5d,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.068642884365467,0.046837036201799465,-10.8851 +7,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)nc1,-9.886459817267562,0.04826796430239271,-8.39681 +5c,CC(C)(O)c1ccc(-c2nc3cccc(Cl)c3c(=O)[nH]2)cc1,-10.811209299511537,0.052188094017022305,-9.96041 +5j,CC(C)(O)c1ccc(-c2nc3ccc(F)c(F)c3c(=O)[nH]2)cc1,-11.069400728762595,0.04426130912758905,-11.0844 +5n,CC(C)(OCCO)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.193713391247433,0.05747706486209336,-10.7146 +5e,CC(C)(O)c1ccc(-c2nc3ccc(Cl)cc3c(=O)[nH]2)cc1,-9.62046076871923,0.039281398912677463,-10.1076 +5k,CC(C)(O)c1ccc(-c2nc3c(F)cc(F)cc3c(=O)[nH]2)cc1,-10.562535132925078,0.0417715515259248,-10.9634 +5p,COCCOC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.214355211199406,0.059366381501473976,-10.5033 +5f,CC(C)(O)c1ccc(-c2nc3c(F)cccc3c(=O)[nH]2)cc1,-11.461912186644616,0.0356727506232857,-10.2631 +5g,CC(C)(O)c1ccc(-c2nc3c(Cl)cccc3c(=O)[nH]2)cc1,-12.039737888715425,0.050527384032239296,-10.806 +5h,COc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-10.179386773020182,0.05357733650415769,-10.0498 +5i,Cc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.635206472400009,0.04819612039768236,-12.0789 +5l,CC(C)(O)c1ccc(-c2nc3c(F)ccc(F)c3c(=O)[nH]2)cc1,-11.708109697043374,0.0460031705398269,-10.0926 +5m,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-10.7849960061047,0.04558151313461519,-12.6889 +5o_adjust,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)OCCO)cc3)nc12,-10.900693309880157,0.05245222211275484,-12.038 diff --git a/summaries/jan_14_2026/merck/tnks2_positive_1/README.md b/summaries/jan_14_2026/merck/tnks2_positive_1/README.md new file mode 100644 index 0000000..35f9292 --- /dev/null +++ b/summaries/jan_14_2026/merck/tnks2_positive_1/README.md @@ -0,0 +1,39 @@ +# Tnks2 Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.85 +- RMSE: 0.93 +- R²: 0.06 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.03 + +## System Details +- Ligands: 6 +- Host Atoms: 3286 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.52 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 752.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/merck/tnks2_positive_1/ddg_results.csv b/summaries/jan_14_2026/merck/tnks2_positive_1/ddg_results.csv new file mode 100644 index 0000000..6b1d9fb --- /dev/null +++ b/summaries/jan_14_2026/merck/tnks2_positive_1/ddg_results.csv @@ -0,0 +1,10 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +8b,8a,-0.31014247372233317,0.04602813835775428,-0.9776493997507346,0.04775958688609393,0.6675069260284014,0.06632923684327241,1.1240000000000012 +8c_adjust,8a,9.660778000925957,0.06406557194584263,9.2131567656512,0.06357655310239513,0.4476212352747569,0.09025727457180172,-0.6829999999999985 +8c_adjust,8d,-0.9277393144566132,0.03428204418712654,-0.663013426108598,0.034112021123703734,-0.26472588834801514,0.04836205680894999,-2.366499999999999 +8c_adjust,8e,10.014657999123184,0.0525255262831674,10.066747221733861,0.048999134627625354,-0.052089222610677194,0.07183206878254213,-0.12060000000000119 +8d,8b,10.388735979639312,0.059463651522765434,10.661634628549526,0.05965318435448783,-0.2728986489102137,0.08422842902518957,0.5594999999999993 +8d,8f,9.957374388829795,0.050953940148010454,9.932868130292167,0.050721229922982454,0.024506258537627022,0.07189539054422808,0.6784000000000001 +8e,8a,0.9202930067608114,0.055199786887814975,-1.004543288321106,0.05781688891932745,1.9248362950819176,0.07993628160460078,-0.5623999999999973 +8f,8b,1.942450669867542,0.04830526773135162,0.5650912160186363,0.04976357846543547,1.3773594538489056,0.06935281272077659,-0.11890000000000081 +8f,8e,1.1801981087988893,0.034099871554724534,0.6679253069096632,0.03340153840782559,0.5122728018892261,0.04773325892978772,1.567499999999998 diff --git a/summaries/jan_14_2026/merck/tnks2_positive_1/dg_comparison_plot.png b/summaries/jan_14_2026/merck/tnks2_positive_1/dg_comparison_plot.png new file mode 100644 index 0000000..31a9df2 Binary files /dev/null and b/summaries/jan_14_2026/merck/tnks2_positive_1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/merck/tnks2_positive_1/dg_plot.png b/summaries/jan_14_2026/merck/tnks2_positive_1/dg_plot.png new file mode 100644 index 0000000..6890efe Binary files /dev/null and b/summaries/jan_14_2026/merck/tnks2_positive_1/dg_plot.png differ diff --git a/summaries/jan_14_2026/merck/tnks2_positive_1/dg_results.csv b/summaries/jan_14_2026/merck/tnks2_positive_1/dg_results.csv new file mode 100644 index 0000000..78b75ce --- /dev/null +++ b/summaries/jan_14_2026/merck/tnks2_positive_1/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +8b,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(N4CC[NH+](C)CC4)cc3)nc12,-10.99421381491495,0.03339805052948228,-11.93 +8a,C[NH+]1CCN(c2ccc(-c3nc4ccc(F)cc4c(=O)[nH]3)cc2)CC1,-10.210993418044746,0.03474544151512433,-10.806 +8c_adjust,O=c1[nH]c(-c2ccc(C3CC[NH2+]CC3)cc2)nc2c(F)cc(F)cc12,-11.187094273110302,0.03337028668238448,-10.123 +8d,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C4CC[NH2+]CC4)cc3)nc12,-11.461191088948722,0.03183793052564665,-12.4895 +8e,C[N@H+]1CC[C@H](c2ccc(-c3nc4c(F)cc(F)cc4c(=O)[nH]3)cc2)CC1,-11.553244771309956,0.03297663227715979,-10.2436 +8f,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc([C@H]4CC[N@H+](C)CC4)cc3)nc12,-11.996462633671333,0.03215499103890713,-11.8111 diff --git a/summaries/jan_14_2026/miscellaneous_set/btk/README.md b/summaries/jan_14_2026/miscellaneous_set/btk/README.md new file mode 100644 index 0000000..fe8c840 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/btk/README.md @@ -0,0 +1,39 @@ +# Btk Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.56 +- RMSE: 1.78 +- R²: 0.71 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 6 +- Host Atoms: 4386 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 16 + - Mean Dummy Atoms: 11.3 + - Median Dummy Atoms: 11.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.45 Hours +- Average Time Per Edge: 0.35 Hours +- Total Nanoseconds Simulated: 1384.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/miscellaneous_set/btk/ddg_results.csv b/summaries/jan_14_2026/miscellaneous_set/btk/ddg_results.csv new file mode 100644 index 0000000..d2c30d6 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/btk/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +10,11,-0.015704686320442442,0.045407280177126294,2.3746216773518762,0.04529568863823184,-2.390326363672319,0.06413673286265595,-0.6547000000000002 +2,10,11.00369272236836,0.06663965486809571,14.573239211156386,0.06507684570641087,-3.5695464887880264,0.09314418633513805,-3.1821700000000006 +2,7,5.796042856025286,0.06079970476565645,5.29115315163325,0.058262445989383224,0.5048897043920362,0.08420876861857549,-1.39668 +2,8,12.968860380749865,0.0638470799905507,15.41141169127877,0.06069131322300109,-2.4425513105289056,0.08809021014875719,-1.9184599999999996 +7,10,-11.233736723203922,0.07296841102736704,-4.919119192736699,0.0711700603279482,-6.314617530467223,0.10192922296840375,-1.785490000000001 +7,9 flip,24.75286814445657,0.07603411778264492,27.633216532510723,0.07526554004653181,-2.880348388054154,0.10698639439424623,0.7536999999999993 +8,10,24.065949218808765,0.06509495750627664,27.948977903913523,0.06135084295671846,-3.883028685104755,0.08944987101300869,-1.2637100000000012 +8,11,24.320572556449612,0.05801264275428657,30.275396333235967,0.05761899411230687,-5.954823776786355,0.08176438834755954,-1.9184100000000013 +9 flip,10,-6.975479493394192,0.07366544612881899,-3.9826270467207343,0.07227600384697082,-2.9928524466734574,0.10320086572042539,-2.53919 +9 flip,11,-5.688767907285669,0.07698464652283518,-1.673718366289427,0.07559815238586144,-4.015049540996243,0.1078967860707714,-3.1938900000000006 diff --git a/summaries/jan_14_2026/miscellaneous_set/btk/dg_comparison_plot.png b/summaries/jan_14_2026/miscellaneous_set/btk/dg_comparison_plot.png new file mode 100644 index 0000000..f01d4b3 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/btk/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/btk/dg_plot.png b/summaries/jan_14_2026/miscellaneous_set/btk/dg_plot.png new file mode 100644 index 0000000..cab2f66 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/btk/dg_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/btk/dg_results.csv b/summaries/jan_14_2026/miscellaneous_set/btk/dg_results.csv new file mode 100644 index 0000000..9722e0a --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/btk/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,NC(=O)c1nnc2c(-c3ccc4cn[nH]c4c3)cccc2c1N,-11.870892771525373,0.029251049339150764,-10.8701 +11,Cc1cc2cn[nH]c2cc1-c1cccc2c(N)c(C(N)=O)nnc12,-14.17114966684597,0.04432940519892751,-11.5248 +2,NC(=O)c1nnc2ccccc2c1N,-6.976375798820403,0.04333722670224299,-7.687929999999999 +7,Cn1cc(-c2cccc3c(N)c(C(N)=O)nnc23)cn1,-6.201125141538394,0.04586135477268322,-9.08461 +8,Cc1ccncc1-c1cccc2c(N)c(C(N)=O)nnc12,-8.529699669823577,0.04574374209290809,-9.60639 +9 flip,NC(=O)c1nnc2c(-c3ccc4cc[nH]c4c3)cccc2c1N,-9.355496951446282,0.04962670936795006,-8.33091 diff --git a/summaries/jan_14_2026/miscellaneous_set/cdk8/README.md b/summaries/jan_14_2026/miscellaneous_set/cdk8/README.md new file mode 100644 index 0000000..b808209 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/cdk8/README.md @@ -0,0 +1,39 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.53 +- RMSE: 1.77 +- R²: 0.00 +- Kendall 𝜏: -0.02 +- Spearman ρ: -0.14 + +## System Details +- Ligands: 10 +- Host Atoms: 10498 +- Map Details: + - Edges: 16 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.84 Hours +- Average Time Per Edge: 0.30 Hours +- Total Nanoseconds Simulated: 1357.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/miscellaneous_set/cdk8/ddg_results.csv b/summaries/jan_14_2026/miscellaneous_set/cdk8/ddg_results.csv new file mode 100644 index 0000000..e92c3ff --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/cdk8/ddg_results.csv @@ -0,0 +1,17 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +12,14,-3.7585467250443916,0.03879471334119764,-4.545896154415162,0.038843544758817954,0.7873494293707711,0.054898549640732694,-1.1986399999999986 +12,15,5.376494981054092,0.04621698631127769,5.668046499940251,0.046252026552185556,-0.29155151888615854,0.0653854707399198,0.11278000000000013 +12,22,-4.981252469075002,0.0512926300431757,-5.3374415598541285,0.050617566998255314,0.35618909077912647,0.07206297236146282,-1.4571400000000003 +13,19,15.05246964949885,0.0461257618741985,15.83952908777034,0.04495324309011256,-0.7870594382714895,0.06440791855660309,0.9724000000000009 +13,20,19.51170695965272,0.05028981691597217,19.13490263604115,0.049984348379731064,0.37680432361156985,0.0709048712599376,0.9141000000000022 +13,21,25.14633111573215,0.05146950291014253,22.36898445231148,0.04741634105628686,2.7773466634206674,0.06998156277894405,1.3348600000000013 +14,17,9.592549334093171,0.05069458857998781,7.726273355087781,0.0422809102001901,1.8662759790053898,0.06601224642936164,0.6362999999999984 +14,19,5.763591401609845,0.05057686185470509,8.743606085520222,0.048304069146080125,-2.980014683910377,0.0699378441985397,0.8067999999999983 +14,20,11.688081936752955,0.04802343252493811,13.404662061870578,0.04562442618611669,-1.7165801251176231,0.06624076038429581,0.7484999999999996 +15,21,27.16994397253825,0.06519498440860319,28.48062073136721,0.061021640971768806,-1.310676758828959,0.08929740566738467,-0.14216000000000015 +15,22,-10.829477640207042,0.05734633310256107,-10.68725996831093,0.0564021948347671,-0.14221767189611292,0.08043512604881602,-1.5699200000000004 +16,17,27.725366961917892,0.05502769484973779,27.23882076191579,0.0535918644114225,0.48654620000210425,0.07681233710523429,0.24020000000000016 +16,20,6.720609234922193,0.05621150359010238,11.098161090129606,0.054520556126054734,-4.377551855207412,0.07830851917993582,0.3524000000000014 +16,22,-5.488578346726696,0.05704572297413487,-2.7864176420165965,0.05248321692479129,-2.7021607047100997,0.07751582140709364,-0.6546 +17,22,-10.035224048044947,0.05658843696818877,-8.20663441347684,0.052283395962665014,-1.8285896345681085,0.0770441736401364,-0.8948000000000002 +19,21,10.26244460849981,0.047557764884607764,7.901365638260293,0.04637713732372455,2.3610789702395176,0.0664272524432799,0.3624600000000003 diff --git a/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_comparison_plot.png b/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_comparison_plot.png new file mode 100644 index 0000000..9d85ae7 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_plot.png b/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_plot.png new file mode 100644 index 0000000..7a84b08 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_results.csv b/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_results.csv new file mode 100644 index 0000000..9b1c77b --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/cdk8/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12,COC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-10.355534621971044,0.03905747251339867,-9.83296 +14,CNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-9.886404700889385,0.031018764508739943,-11.0316 +15,CN(C)C(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-10.105377319329817,0.0437746708726953,-9.72018 +22,CNC(=O)c1cc2c(Oc3ccc(I)cc3)cncc2s1,-10.109034247093726,0.03885553371108228,-11.2901 +13,NC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-12.659528018482177,0.04463742377189496,-11.1972 +19,CC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-13.098475477515931,0.03785478318648434,-10.2248 +20,CCC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.99188929970572,0.0443477456509216,-10.2831 +21,O=C(c1cc2c(Oc3ccc(Cl)cc3)cncc2s1)C1CC1,-10.576458417984846,0.04370015448453407,-9.86234 +17,O=C(NC1CC1)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-7.887268153569503,0.04921324527485727,-10.3953 +16,CCNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-7.803109743457837,0.04353058624805982,-10.6355 diff --git a/summaries/jan_14_2026/miscellaneous_set/faah/README.md b/summaries/jan_14_2026/miscellaneous_set/faah/README.md new file mode 100644 index 0000000..e6dddd2 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/faah/README.md @@ -0,0 +1,39 @@ +# Faah Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.98 +- RMSE: 1.19 +- R²: 0.56 +- Kendall 𝜏: 0.32 +- Spearman ρ: 0.44 + +## System Details +- Ligands: 24 +- Host Atoms: 8440 +- Map Details: + - Edges: 41 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 6.0 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 9.69 Hours +- Average Time Per Edge: 0.24 Hours +- Total Nanoseconds Simulated: 3738.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/miscellaneous_set/faah/ddg_results.csv b/summaries/jan_14_2026/miscellaneous_set/faah/ddg_results.csv new file mode 100644 index 0000000..b8c9e84 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/faah/ddg_results.csv @@ -0,0 +1,42 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +11,12,3.2879997463469866,0.04847715525878926,4.846697059803434,0.046731876100410186,-1.5586973134564472,0.06733426190171575,1.0765999999999996 +11,24,9.725596025735854,0.06155114255780745,9.775115447923321,0.06184930903812563,-0.04951942218746779,0.08725755084040066,0.4954999999999999 +11,25,6.089591833279577,0.06414893510835118,5.991129489761759,0.06321807669980722,0.09846234351781821,0.0900644829950084,0.0847999999999998 +12,27,5.510394751383232,0.06564430146906176,5.4825684418394065,0.06582046101836582,0.027826309543825638,0.09295970849799004,-0.14149999999999835 +14,19,1.2997401709552319,0.0521263852124642,2.4765466005310235,0.054002252739410624,-1.1768064295757914,0.07505600133399987,-0.12979999999999955 +14,20,7.632436896372697,0.05050228816356683,6.579371681285368,0.050024651238762693,1.0530652150873299,0.0710840828970578,1.0212900000000014 +14,30,-0.39115703949199343,0.05323547262964347,3.01528022552682,0.0569862259358899,-3.4064372650188135,0.07798362323281606,-2.06142 +15,14,5.7768835575011,0.03997652393493777,1.0803140237009425,0.0421603027761586,4.696569533800157,0.058100030947479016,0.7477499999999996 +19,30,6.254218685382524,0.05241561784648973,7.899966357795511,0.05418648575053607,-1.6457476724129871,0.07538947030071443,-1.9316200000000003 +22,28,-2.4313850990940757,0.05465577891444825,-0.6634899435169223,0.053635391560738856,-1.7678951555771534,0.07657682023052943,-1.6167200000000008 +22,29,2.9470771092040966,0.04900291366785589,5.597129347961127,0.05086851745433318,-2.650052238757031,0.07063208630602055,-0.8336199999999991 +22,31,3.796729384410058,0.05127063649936698,6.926582448606122,0.05158849567607856,-3.1298530641960634,0.07273273714890013,-1.317720000000001 +23,24,2.4623640180776265,0.056209939586043256,2.4246615465304,0.05604294815195679,0.03770247154722657,0.07937486595786823,-0.9535999999999999 +23,27,2.776166497499484,0.0515925618497547,2.909696727829152,0.05132064746122016,-0.13353023032966774,0.07277088218552533,-0.5139999999999985 +24,27,-0.14489096209176702,0.04824589079197189,0.8258299294985346,0.04952451796393087,-0.9707208915903017,0.06914003079165203,0.43960000000000143 +25,26,1.5964661684351178,0.04377765233080705,1.8264913738025503,0.04497589089154326,-0.23002520536743248,0.06276395147761986,1.3643 +25,28,-5.214190690731977,0.05861704624829543,-4.601887551832088,0.05778982542397652,-0.6123031388998894,0.08231416666290492,0.44889999999999997 +26,28,-6.061548221845255,0.05155004843924074,-6.469207077558742,0.052682018458513655,0.4076588557134866,0.07370754753043436,-0.9154 +28,33 (Saha 2018),8.309424359969514,0.06110656009409907,8.582749894285996,0.062169352450348325,-0.273325534316483,0.08717247312442944,1.8529100000000003 +29,39,1.0929613475831887,0.054867084494905315,2.476346349539227,0.0547365973964964,-1.3833850019560383,0.07750156163276463,0.09139999999999748 +2,14,-1.039395928522277,0.030638149276771474,-2.1307214321940777,0.03445905813797147,1.091325503671801,0.046109900009236954,0.8226899999999993 +2,15,-6.263535703781303,0.04114184987682657,-2.5656676416111357,0.04190982502688067,-3.697868062170167,0.058728913195044634,0.07493999999999965 +2,20,6.169155740935506,0.05228550077274316,4.279648209744866,0.05471129904188826,1.88950753119064,0.07567760457300064,1.8439800000000006 +30,31,-0.6840819456241876,0.04620243873594284,0.5488526505245678,0.04655797951602815,-1.2329345961487552,0.06559200257473047,-1.3861599999999996 +31,39,-0.07493357446857574,0.046544630086064936,1.437742552222479,0.045917929835967326,-1.5126761266910547,0.06538240489817913,0.5754999999999992 +33 (Saha 2018),39,0.7317268551670456,0.05089422747370082,1.5706012473725885,0.051323222990619546,-0.8388743922055429,0.07227928893043749,-0.978410000000001 +4,14,0.3750715417115277,0.042210324720125175,-4.38153930508712,0.04571054190343626,4.756610846798647,0.0622186881417811,3.48218 +4,28,-8.977983864755801,0.05994044017578045,-9.770575879327595,0.059636257525757644,0.7925920145717942,0.08455376739178924,-0.2643999999999995 +4,6,-0.16081282151555612,0.05029687893019452,-0.9035507940428582,0.05003262878416064,0.7427379725273021,0.07094392132644112,0.9042000000000006 +6MRG ligand,19,-13.300639009950178,0.061090982445737,-15.520432692184794,0.06193679548471759,2.2197936822346156,0.086995831917978,2.3149799999999994 +6MRG ligand,26,-9.754695021796211,0.0660367672562575,-8.750268760223719,0.06634215003605526,-1.0044262615724915,0.09360627917540355,-0.38640000000000047 +6MRG ligand,9,-11.602340380615699,0.07073819405204988,-7.908677322060137,0.07028940847324527,-3.6936630585555625,0.09972207900592621,-0.2784000000000001 +6,15,-5.5865902085287935,0.047700030935328104,-4.510190175050157,0.047420591146006746,-1.0764000334786357,0.06726072714346755,1.8302299999999998 +6,20,7.247917182798164,0.05343175526017259,3.354372422811168,0.05526582847610957,3.893544759986997,0.07687173906796792,3.5992700000000006 +6,29,-1.3750067569387083,0.04036035180887833,-0.900329442797214,0.04164031441954847,-0.4746773141414942,0.05799029042085653,-0.38549999999999846 +6,33 (Saha 2018),-1.6766378431291926,0.049680966705494295,0.49992046402180185,0.05232238290964759,-2.1765583071509944,0.07215143939060546,0.6843100000000001 +9,12,-3.116571615953236,0.06190548497947377,-2.709973394243384,0.06378091020437782,-0.40659822170985205,0.08888359565770704,-0.48050000000000054 +9,14,-3.127823126690332,0.04342063909665896,-9.015105428736383,0.04699296606642747,5.887282302046052,0.06398195651340081,2.7231799999999993 +fig 3,12,-3.080491365274785,0.052154079339295875,-1.7272369023711356,0.05239432995533745,-1.3532544629036494,0.07392708436830402,-0.4466 +fig 3,14,-3.012104610117509,0.041471022991771904,-7.601129255195014,0.04092666839366767,4.589024645077505,0.05826523778196833,2.7570799999999998 +fig 3,23,0.569705723922566,0.0428277827610584,0.8329436703809552,0.041735428218947386,-0.2632379464583891,0.05980020856859382,-0.07409999999999982 diff --git a/summaries/jan_14_2026/miscellaneous_set/faah/dg_comparison_plot.png b/summaries/jan_14_2026/miscellaneous_set/faah/dg_comparison_plot.png new file mode 100644 index 0000000..c679a74 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/faah/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/faah/dg_plot.png b/summaries/jan_14_2026/miscellaneous_set/faah/dg_plot.png new file mode 100644 index 0000000..92d3ad4 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/faah/dg_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/faah/dg_results.csv b/summaries/jan_14_2026/miscellaneous_set/faah/dg_results.csv new file mode 100644 index 0000000..0b59596 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/faah/dg_results.csv @@ -0,0 +1,25 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +11,CCSc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1,-10.845527254424598,0.056170457619651434,-12.1228 +12,O[C@@H](CNc1cc(-c2ccc(SC(F)(F)F)cc2)ncn1)c1ccccc1,-12.460897928649228,0.0561133520220991,-11.0462 +24,CCOc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1C(F)(F)F,-11.126038760269948,0.06092365439264588,-11.6273 +25,CCOc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1Cl,-10.399578150126636,0.05129194411384284,-12.038 +27,O[C@@H](CNc1cc(-c2ccc(OCC(F)(F)F)c(F)c2)ncn1)c1ccccc1,-11.997157465216958,0.06162669249012591,-11.1877 +14,O[C@@H](CNc1cc(-c2ccc(F)cc2)ncn1)c1ccccc1,-6.520681066714911,0.027844175245980277,-7.84252 +19,COc1cccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)c1,-7.728622349826906,0.05285506756653356,-7.972320000000001 +20,Cc1ccccc1-c1cc(NC[C@H](O)c2ccccc2)ncn1,-5.744415166156589,0.04688166136084928,-6.82123 +30,O[C@@H](CNc1cc(-c2ccc(Cl)c(C(F)(F)F)c2)ncn1)c1ccccc1,-9.713401942330085,0.04511419459433897,-9.90394 +15,N#CCc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1,-11.205477549225828,0.040664496316420405,-8.59027 +22,COc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1C,-8.248827180664101,0.052706784611043604,-9.97238 +28,CC(=O)c1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1F,-10.559028588660142,0.042690664855708396,-11.5891 +29,O[C@@H](CNc1cc(-c2ccc(C(F)(F)F)c(F)c2)ncn1)c1ccccc1,-10.74579336194024,0.05040471740501991,-10.806 +31,O[C@@H](CNc1cc(-c2ccc(C(F)(F)F)c(Cl)c2)ncn1)c1ccccc1,-11.051781165877934,0.054160605755989535,-11.2901 +23,O[C@@H](CNc1cc(-c2ccc(OC(F)(F)F)c(F)c2)ncn1)c1ccccc1,-11.486156749063868,0.05706242788770726,-10.6737 +26,CCOc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1F,-10.72413663146006,0.05228845522304383,-10.6737 +33 (Saha 2018),O[C@@H](CNc1cc(-c2ccc(C(F)(F)F)c(Cl)c2)ncn1)c1cccc(F)c1,-11.611353473437092,0.0550200921946483,-9.73619 +39,O[C@@H](CNc1cc(-c2ccc(C(F)(F)F)c(Cl)c2)ncn1)c1ccc(F)c(F)c1,-12.405063895960472,0.05841213132129569,-10.7146 +2,Cc1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1,-7.583723469301021,0.039196241057229624,-8.66521 +4,CC(C)c1ccc(-c2cc(NC[C@H](O)c3ccccc3)ncn2)cc1,-11.121251841517317,0.043119971331686706,-11.3247 +6,O[C@@H](CNc1cc(-c2ccc(C(F)(F)F)cc2)ncn1)c1ccccc1,-10.013464061980539,0.03607314281065605,-10.4205 +6MRG ligand,O[C@@H](CNc1cc(-c2ccc3c(c2)OCCO3)ncn1)c1ccccc1,-9.53878788776362,0.057058596437485835,-10.2873 +9,O[C@@H](CNc1cc(-c2ccc(OCC(F)(F)F)cc2)ncn1)c1ccccc1,-12.48887539980178,0.05149279332677265,-10.5657 +fig 3,O[C@@H](CNc1cc(-c2ccc(OC(F)(F)F)cc2)ncn1)c1ccccc1,-11.151018659630159,0.04567611321906084,-10.5996 diff --git a/summaries/jan_14_2026/miscellaneous_set/galectin/README.md b/summaries/jan_14_2026/miscellaneous_set/galectin/README.md new file mode 100644 index 0000000..dccdb8a --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/galectin/README.md @@ -0,0 +1,39 @@ +# Galectin Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.70 +- RMSE: 0.94 +- R²: 0.56 +- Kendall 𝜏: 0.49 +- Spearman ρ: 0.69 + +## System Details +- Ligands: 26 +- Host Atoms: 2225 +- Map Details: + - Edges: 45 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 4.4 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.71 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 4006.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/miscellaneous_set/galectin/ddg_results.csv b/summaries/jan_14_2026/miscellaneous_set/galectin/ddg_results.csv new file mode 100644 index 0000000..7111e68 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/galectin/ddg_results.csv @@ -0,0 +1,46 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +17a,17b,0.8682250001430244,0.04138519265708585,1.4459621938609233,0.04226576215522296,-0.5777371937178989,0.0591534345733702,0.02634000000000041 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100644 index 0000000..efc6501 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/README.md @@ -0,0 +1,39 @@ +# Hiv1 Protease Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.06 +- RMSE: 1.25 +- R²: 0.02 +- Kendall 𝜏: 0.12 +- Spearman ρ: 0.16 + +## System Details +- Ligands: 13 +- Host Atoms: 3128 +- Map Details: + - Edges: 22 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 7.5 + - Median Dummy Atoms: 7.5 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 5.29 Hours +- Average Time Per Edge: 0.24 Hours +- Total Nanoseconds Simulated: 2333.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/ddg_results.csv b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/ddg_results.csv new file mode 100644 index 0000000..038c06e --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/ddg_results.csv @@ -0,0 +1,23 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +10,11 (2cen),4.367220495091188,0.044439963959653654,5.128505878596438,0.04241762890702875,-0.76128538350525,0.061434238327090177,-0.5187000000000022 +10,17,-0.7917927966052362,0.07041928115302157,1.4904437416535956,0.07184391075041882,-2.2822365382588314,0.10060031148074267,-0.6813000000000015 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+14,16,-8.049967068966119,0.0357668576769398,-7.8733702777139225,0.03751102950741571,-0.1765967912521949,0.05182996664853914,-0.3874999999999995 +15,16,2.935475751828263,0.041784414868355615,3.2342630743878478,0.041458523547837356,-0.29878732255958446,0.05886209731786188,-0.0847999999999998 +17,18,12.687419975786495,0.06986727010008117,12.372659297082077,0.06982120632062735,0.31476067870441754,0.09877467430118568,-0.35129999999999895 +19,20,6.34888942470688,0.0781823434496122,5.3621454011012455,0.07797603035376277,0.986744023605635,0.11042074142571247,-0.6785000000000003 +1,13,18.729033980581796,0.06637591520123311,17.674514774767616,0.06329580949023073,1.0545192058141795,0.09171761890621055,0.9019999999999991 +1,14,4.27957446885976,0.06571516873549157,5.752063372069538,0.06281562291360926,-1.4724889032097785,0.09090811781111124,1.085799999999998 +1,15,-4.561698401754267,0.06484767408356498,-1.700708452200355,0.06346808578829717,-2.860989949553912,0.09073818792371222,0.7830999999999984 +1,16,-0.11851630740698253,0.06418083011399328,1.9358085963895042,0.06372614740987748,-2.054324903796487,0.09044446261561125,0.6982999999999985 +1,17,1.0606118255546761,0.05848606913720817,0.9371687430703186,0.056008091627586895,0.12344308248435747,0.08097855648803863,0.27219999999999817 +1,18,25.052653656920235,0.05852594334134926,25.01255447668897,0.0552260641520521,0.04009918023126686,0.08046865355976449,-0.07910000000000074 +1,20,11.359215086618091,0.061819473631945066,11.691492209831667,0.05876308879770038,-0.3322771232135752,0.08529213284457818,0.22349999999999873 +9,11 (2cen),-6.173903659311486,0.03814814643010835,-5.924749901935617,0.03829180459559492,-0.24915375737587003,0.054051303178001296,-0.8214000000000018 +9,12,-12.254278554582779,0.03841401462580217,-12.14118313316912,0.03733191425057931,-0.11309542141366034,0.05356592518835038,-0.764900000000002 +9,19,5.659862504004534,0.057795945873689816,6.641283482837579,0.057003899533675996,-0.9814209788330465,0.0811776811782642,-0.3542000000000003 diff --git a/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_comparison_plot.png b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_comparison_plot.png new file mode 100644 index 0000000..b9afd14 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_plot.png b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_plot.png new file mode 100644 index 0000000..b0218dd Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_results.csv b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_results.csv new file mode 100644 index 0000000..8c29708 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/hiv1_protease/dg_results.csv @@ -0,0 +1,14 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccccn2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-9.723526634895077,0.04890309728444783,-10.806 +11 (2cen),COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2cccnc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.483606520823988,0.049942607147905486,-11.3247 +17,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2c(C)noc2C)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-11.15828341090621,0.05475209060174229,-11.4873 +18,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2cnccn2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.545844727843438,0.052943950950344994,-11.8386 +12,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccncc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.263405736653857,0.05462934171080042,-11.2682 +19,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccc3c(c2)OCO3)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-11.256234863120634,0.048822755097195386,-10.8575 +13,COC(=O)N[C@H](C(=O)NN(Cc1ccc(/C=C/c2ccccc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.229060231469504,0.0543356858488771,-10.8575 +20,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2cc3ccccc3s2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.96382214063954,0.056042482769351254,-11.536 +14,COC(=O)N[C@H](C(=O)NN(Cc1ccc(C#Cc2ccccc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-12.933066817337107,0.05651242647848521,-10.6737 +15,COC(=O)N[C@H](C(=O)NN(Cc1ccc(C#Cc2ccccn2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-13.068126909859709,0.055871280007096735,-10.9764 +16,COC(=O)N[C@H](C(=O)NN(Cc1ccc(C#Cc2cccnc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-13.18532659446008,0.058894176657519406,-11.0612 +1,COC(=O)N[C@H](C(=O)NN(Cc1ccc(Br)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.932678363048526,0.03897756586045274,-11.7595 +9,COC(=O)N[C@H](C(=O)NN(Cc1ccc(-c2ccccc2)cc1)C[C@@](O)(Cc1ccccc1)C(=O)N[C@H]1c2ccccc2C[C@H]1O)C(C)(C)C,-10.206917048942303,0.05214687340060796,-10.5033 diff --git a/summaries/jan_14_2026/miscellaneous_set/malt1/README.md b/summaries/jan_14_2026/miscellaneous_set/malt1/README.md new file mode 100644 index 0000000..61ffb35 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/malt1/README.md @@ -0,0 +1,39 @@ +# Malt1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.16 +- RMSE: 1.47 +- R²: 0.45 +- Kendall 𝜏: 0.42 +- Spearman ρ: 0.53 + +## System Details +- Ligands: 10 +- Host Atoms: 6224 +- Map Details: + - Edges: 16 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 16 + - Mean Dummy Atoms: 10.6 + - Median Dummy Atoms: 12.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.76 Hours +- Average Time Per Edge: 0.30 Hours +- Total Nanoseconds Simulated: 1689.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/miscellaneous_set/malt1/ddg_results.csv b/summaries/jan_14_2026/miscellaneous_set/malt1/ddg_results.csv new file mode 100644 index 0000000..7bcc652 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/malt1/ddg_results.csv @@ -0,0 +1,17 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +1832576-04-1,1832577-09-9,1.0270739731012628,0.04959482448621337,-0.006917346125883325,0.049175899345101526,1.033991319227146,0.06984207680344183,1.645852349536163 +1832576-04-1,Pfizer-01-07,40.86792284027916,0.07347690043324799,40.40908283347955,0.07338945028863884,0.45884000679960324,0.10385021093356543,3.567719050759443 +1832577-09-9,2714550-01-1,-0.347652326508205,0.057805877238181216,0.8874115105603297,0.05769954313305281,-1.2350638370685347,0.08167470061799247,-0.38622292552512305 +1832577-09-9,Pfizer-01-03,25.931252515067893,0.0689523479441875,23.6340230852318,0.06902724060254622,2.297229429836094,0.09756631709877185,0.06179790825459522 +2714550-01-1,Pfizer-01-02,-0.7961094096541216,0.03444443066214016,-2.6427463195984986,0.03909483846224223,1.8466369099443771,0.05210398447362539,0.1869927993991443 +Pfizer-01-01,1832576-04-1,-2.3667703421351307,0.06209350604096361,-0.8926088334765431,0.06363013615997475,-1.4741615086585875,0.08890667984013412,-1.1857247500970411 +Pfizer-01-01,Pfizer-01-02,-3.3469536615607183,0.041098710825066595,-3.094140056272882,0.04302564556945905,-0.2528136052878363,0.05950050594869894,0.26089747331314306 +Pfizer-01-01,Pfizer-01-07,37.19664605379592,0.06860569078009085,38.067400724627625,0.06966648213998829,-0.8707546708317072,0.09777606834586239,2.381994300662402 +Pfizer-01-03,Pfizer-01-06,4.55238059974393,0.04956495170158517,2.9656479458070373,0.04920333057917403,1.5867326539368933,0.06984019027224907,1.6856811149845812 +Pfizer-01-04,Pfizer-01-02,5.786994904383281,0.047315163361441676,8.447357028955299,0.04725581288602495,-2.6603621245720177,0.06687179177679416,-1.397320627271665 +Pfizer-01-04,Pfizer-01-06,14.886340713045655,0.0560905969662069,14.318062502703784,0.05565176845584184,0.5682782103418714,0.07901439362728852,0.5493885220934902 +Pfizer-01-05,Pfizer-01-02,3.761097039692954,0.05811534234565494,7.792242644246928,0.053924794855529104,-4.0311456045539735,0.0792797358482202,-1.913078837871389 +Pfizer-01-05,Pfizer-01-03,13.40700633954999,0.05178098161646484,16.99473604455843,0.054606617670942534,-3.587729705008437,0.07525392182886659,-1.652050803490815 +Pfizer-01-05,Pfizer-01-04,-0.8070195398329036,0.042976444383546517,0.24881759988914298,0.04781384887441657,-1.0558371397220465,0.06428949304542396,-0.515758210599724 +Pfizer-01-05,Pfizer-01-06,18.842884999761008,0.06014574866444728,19.890278011496097,0.06052746626530927,-1.0473930117350898,0.0853292754856445,0.033630311493766114 +Pfizer-01-07,2714550-01-1,-39.056293142918776,0.06919804413787665,-37.97163044080938,0.07097261835925561,-1.0846627021093933,0.09912356868714964,-2.3080896267484032 diff --git a/summaries/jan_14_2026/miscellaneous_set/malt1/dg_comparison_plot.png b/summaries/jan_14_2026/miscellaneous_set/malt1/dg_comparison_plot.png new file mode 100644 index 0000000..70f3f49 Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/malt1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/malt1/dg_plot.png b/summaries/jan_14_2026/miscellaneous_set/malt1/dg_plot.png new file mode 100644 index 0000000..c6ca26a Binary files /dev/null and b/summaries/jan_14_2026/miscellaneous_set/malt1/dg_plot.png differ diff --git a/summaries/jan_14_2026/miscellaneous_set/malt1/dg_results.csv b/summaries/jan_14_2026/miscellaneous_set/malt1/dg_results.csv new file mode 100644 index 0000000..bdf78b4 --- /dev/null +++ b/summaries/jan_14_2026/miscellaneous_set/malt1/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1832576-04-1,CO[C@@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.142437657847378,0.053889461003801466,-10.031196069300446 +1832577-09-9,CO[C@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-9.308089971078024,0.046799879139372,-8.385343719764283 +Pfizer-01-07,Cn1ncc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)c21,-9.481582945401408,0.05702799471902152,-6.463477018541003 +2714550-01-1,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.503480491465417,0.04071888647884317,-8.771566645289406 +Pfizer-01-03,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)n2n1,-7.457076292802193,0.04994724820780763,-8.323545811509687 +Pfizer-01-02,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-8.623355272157417,0.03301775271269181,-8.584573845890262 +Pfizer-01-01,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2ccnn12,-8.492824212472954,0.04684675326526533,-8.845471319203405 +Pfizer-01-06,Cc1nc2c(C3CC3)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1C,-5.583106648726784,0.05468815137340419,-6.6378646965251065 +Pfizer-01-04,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,-5.84153082380389,0.042598905574360114,-7.187253218618596 +Pfizer-01-05,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)cn2n1,-4.468303036905598,0.04544782224155567,-6.671495008018873 diff --git a/summaries/jan_14_2026/scaffold_hopping_set/bace1/README.md b/summaries/jan_14_2026/scaffold_hopping_set/bace1/README.md new file mode 100644 index 0000000..29c49f2 --- /dev/null +++ b/summaries/jan_14_2026/scaffold_hopping_set/bace1/README.md @@ -0,0 +1,39 @@ +# Bace1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.40 +- RMSE: 1.48 +- R²: 0.55 +- Kendall 𝜏: 1.00 +- Spearman ρ: 1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 6049 +- Map Details: + - Edges: 3 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 6.7 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.56 Hours +- Average Time Per Edge: 0.52 Hours +- Total Nanoseconds Simulated: 351.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/scaffold_hopping_set/bace1/ddg_results.csv b/summaries/jan_14_2026/scaffold_hopping_set/bace1/ddg_results.csv new file mode 100644 index 0000000..441f839 --- /dev/null +++ b/summaries/jan_14_2026/scaffold_hopping_set/bace1/ddg_results.csv @@ -0,0 +1,4 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +31,6,-11.475074128583712,0.04026377992576026,-11.846517261827849,0.041188155775058584,0.3714431332441371,0.05759892490368677,0.5199999999999999 +31,7,10.00850006678526,0.06936966802404525,5.643223807374823,0.0683222745221352,4.365276259410436,0.09736572311467856,0.6399999999999998 +7,6,-20.23987039558632,0.06546620703330672,-17.498266724364363,0.06458514270811598,-2.741603671221958,0.09196230163472141,-0.11999999999999986 diff --git a/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_comparison_plot.png b/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_comparison_plot.png new file mode 100644 index 0000000..f8dcdea Binary files /dev/null and b/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_plot.png b/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_plot.png new file mode 100644 index 0000000..2c04612 Binary files /dev/null and b/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_plot.png differ diff --git a/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_results.csv b/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_results.csv new file mode 100644 index 0000000..d7f10a3 --- /dev/null +++ b/summaries/jan_14_2026/scaffold_hopping_set/bace1/dg_results.csv @@ -0,0 +1,4 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +31,NC1=[NH+][C@@H]2CC[C@H](OC(=O)c3cccc(Cl)c3)C[C@@H]2CS1,-9.421219225879735,0.03329482511809302,-8.35 +6,NC1=[NH+][C@@H]2CC[C@H](NC(=O)c3cccc(Cl)c3)C[C@@H]2CS1,-8.854316966333634,0.03406341125809459,-7.829999999999999 +7,NC1=[NH+][C@]23CC[C@H](NC(=O)c4cccc(Cl)c4)C[C@@H]2[C@@H](COC3)S1,-5.6144638077866285,0.04465838052630659,-7.71 diff --git a/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/README.md b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/README.md new file mode 100644 index 0000000..59b79c9 --- /dev/null +++ b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/README.md @@ -0,0 +1,39 @@ +# Factor Xa Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.88 +- RMSE: 2.00 +- R²: 1.00 +- Kendall 𝜏: -1.00 +- Spearman ρ: -1.00 + +## System Details +- Ligands: 3 +- Host Atoms: 4426 +- Map Details: + - Edges: 3 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 6.7 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.37 Hours +- Average Time Per Edge: 0.46 Hours +- Total Nanoseconds Simulated: 388.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/ddg_results.csv b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/ddg_results.csv new file mode 100644 index 0000000..af9005d --- /dev/null +++ b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/ddg_results.csv @@ -0,0 +1,4 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +4d,4c,-0.876211050590389,0.04506493821469758,-1.059041157393158,0.043863173610586205,0.18283010680276895,0.06288741253611042,-0.0699999999999992 +Edoxaban,4c,36.23716754017218,0.06959887466795832,39.02458738828852,0.06848528375349731,-2.78741984811634,0.09764341987990391,0.8000000000000002 +Edoxaban,4d,36.06362421844533,0.07448286580225584,40.14025666187607,0.0737099652243493,-4.076632443430752,0.10478958093003156,0.8699999999999993 diff --git a/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_comparison_plot.png b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_comparison_plot.png new file mode 100644 index 0000000..f43ece4 Binary files /dev/null and b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_plot.png b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_plot.png new file mode 100644 index 0000000..cf0f85e Binary files /dev/null and b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_plot.png differ diff --git a/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_results.csv b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_results.csv new file mode 100644 index 0000000..7153e45 --- /dev/null +++ b/summaries/jan_14_2026/scaffold_hopping_set/factor_xa/dg_results.csv @@ -0,0 +1,4 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +4d,CCN(C)C(=O)[C@H]1CC[C@H](NC(=O)c2cc3cc(Cl)ccc3[nH]2)[C@H](NC(=O)c2nc3c(s2)C[N@H+](C)CC3)C1,-13.347262596073527,0.03718964091428791,-11.72 +4c,CN(C)C(=O)[C@H]1CC[C@H](NC(=O)c2cc3cc(Cl)ccc3[nH]2)[C@H](NC(=O)c2nc3c(s2)C[N@H+](C)CC3)C1,-12.985619036261337,0.033333106681001395,-11.79 +Edoxaban,CN(C)C(=O)[C@H]1CC[C@H](NC(=O)C(=O)Nc2ccc(Cl)cn2)[C@H](NC(=O)c2nc3c(s2)C[N@H+](C)CC3)C1,-9.767118367665136,0.042217281974180884,-12.59 diff --git a/summaries/jan_14_2026/water_set/brd4/README.md b/summaries/jan_14_2026/water_set/brd4/README.md new file mode 100644 index 0000000..2c8f197 --- /dev/null +++ b/summaries/jan_14_2026/water_set/brd4/README.md @@ -0,0 +1,39 @@ +# Brd4 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.63 +- RMSE: 2.02 +- R²: 0.25 +- Kendall 𝜏: -0.07 +- Spearman ρ: -0.14 + +## System Details +- Ligands: 8 +- Host Atoms: 2109 +- Map Details: + - Edges: 13 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.88 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 976.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/brd4/ddg_results.csv b/summaries/jan_14_2026/water_set/brd4/ddg_results.csv new file mode 100644 index 0000000..c9cf465 --- /dev/null +++ b/summaries/jan_14_2026/water_set/brd4/ddg_results.csv @@ -0,0 +1,14 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +cmpd 2 (methyl),cmpd 3 (Allyl),1.2553347876045784,0.04813048017984281,3.459087421219366,0.04936510014324231,-2.2037526336147875,0.06894531336134882,2.5 +cmpd 2 (methyl),cmpd 6 (ethyl),1.5513472223355873,0.044773032085973864,2.7759321491141935,0.04314861021904176,-1.2245849267786064,0.062180599595102325,1.000000000000001 +cmpd 2 (methyl),cmpd 7 (n-propyl),1.6569269459061329,0.04624898334775562,4.672510008689264,0.04624107113774454,-3.0155830627831315,0.06540034495831752,2.570000000000001 +cmpd 3 (Allyl),cmpd 4 (Crotyl),2.2616352704366927,0.039542291859331356,4.397358724672941,0.04162969224941903,-2.135723454236248,0.05741623570271637,-1.5499999999999996 +cmpd 3 (Allyl),cmpd 6 (ethyl),2.345506488637089,0.04665006967455571,1.3920641017091226,0.04733281082969142,0.9534423869279663,0.06645768564793884,-1.4999999999999991 +cmpd 3 (Allyl),cmpd 8 (n-Butyl),10.717348175942284,0.05558779302501977,12.503369640821377,0.056125704640437944,-1.7860214648790935,0.07899428748193196,-0.5700000000000006 +cmpd 5 (1-Butenyl),cmpd 7 (n-propyl),1.1757011757062215,0.04426658679336967,-0.10436974440797317,0.04417275005057949,1.2800709201141947,0.06253609000701835,0.6200000000000004 +cmpd 5 (1-Butenyl),cmpd 8 (n-Butyl),8.054790529527969,0.05290927269503698,8.536469732521146,0.052278358129201015,-0.48167920299317735,0.07438022496472288,-0.020000000000001107 +cmpd 5 (1-Butenyl),cmpd 9 (methoxyethyl),-3.756590734701134,0.050657398812349284,-5.235327952540168,0.049134248489775885,1.4787372178390348,0.07057156955239446,0.4199999999999995 +cmpd 6 (ethyl),cmpd 7 (n-propyl),1.0108903428333254,0.041261567296421296,2.616622374387893,0.041035508064824505,-1.6057320315545676,0.05819303960007056,1.57 +cmpd 8 (n-Butyl),cmpd 4 (Crotyl),-8.873810126294781,0.05425246872106499,-9.05776134893593,0.0555549997585032,0.1839512226411488,0.07765106799328278,-0.9799999999999991 +cmpd 9 (methoxyethyl),cmpd 4 (Crotyl),3.175472944735673,0.0512067535513283,4.794335420182528,0.052678118194872316,-1.618862475446855,0.07346506479830678,-1.4199999999999997 +cmpd 9 (methoxyethyl),cmpd 8 (n-Butyl),10.538294984981698,0.039938664180048544,12.09822938632825,0.04082641986418193,-1.559934401346551,0.057112988500105315,-0.4400000000000006 diff --git a/summaries/jan_14_2026/water_set/brd4/dg_comparison_plot.png b/summaries/jan_14_2026/water_set/brd4/dg_comparison_plot.png new file mode 100644 index 0000000..330906d Binary files /dev/null and b/summaries/jan_14_2026/water_set/brd4/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/water_set/brd4/dg_plot.png b/summaries/jan_14_2026/water_set/brd4/dg_plot.png new file mode 100644 index 0000000..6569393 Binary files /dev/null and b/summaries/jan_14_2026/water_set/brd4/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/brd4/dg_results.csv b/summaries/jan_14_2026/water_set/brd4/dg_results.csv new file mode 100644 index 0000000..e068e06 --- /dev/null +++ b/summaries/jan_14_2026/water_set/brd4/dg_results.csv @@ -0,0 +1,9 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 2 (methyl),CN(C)C(=O)c1cccc(-c2cn(C)c(=O)c3[nH]ccc23)c1,-5.191242802911713,0.04003068024867378,-9.59 +cmpd 3 (Allyl),C=CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.459070264357916,0.032660568523720526,-7.09 +cmpd 6 (ethyl),CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-6.468234527863519,0.03988170307620421,-8.59 +cmpd 7 (n-propyl),CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.091196109153037,0.038079196192810374,-7.02 +cmpd 4 (Crotyl),C/C=C/Cn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.513330248041822,0.03830519413062483,-8.64 +cmpd 8 (n-Butyl),CCCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.53623788729986,0.033941426969479,-7.660000000000001 +cmpd 5 (1-Butenyl),C=CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.28544092519588,0.042172587227431134,-7.64 +cmpd 9 (methoxyethyl),COCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.90524723517625,0.04163965370270926,-7.22 diff --git a/summaries/jan_14_2026/water_set/chk1/README.md b/summaries/jan_14_2026/water_set/chk1/README.md new file mode 100644 index 0000000..40a5099 --- /dev/null +++ b/summaries/jan_14_2026/water_set/chk1/README.md @@ -0,0 +1,39 @@ +# Chk1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.87 +- RMSE: 2.38 +- R²: 0.09 +- Kendall 𝜏: -0.19 +- Spearman ρ: -0.24 + +## System Details +- Ligands: 13 +- Host Atoms: 4342 +- Map Details: + - Edges: 22 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 5.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 5.62 Hours +- Average Time Per Edge: 0.26 Hours +- Total Nanoseconds Simulated: 2349.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/chk1/ddg_results.csv b/summaries/jan_14_2026/water_set/chk1/ddg_results.csv new file mode 100644 index 0000000..73a1b6d --- /dev/null +++ b/summaries/jan_14_2026/water_set/chk1/ddg_results.csv @@ -0,0 +1,23 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +12 docked,11 docked,7.182780705068278,0.05656480441589565,4.432456776182512,0.05782130047127383,2.7503239288857655,0.0808880701141884,-2.366270000000001 +13 docked,12 docked,-0.47940547987964777,0.046536571841584974,0.28447418325115,0.04613877998293623,-0.7638796631307978,0.06553197339528848,1.3084200000000006 +14 docked,11 docked,8.492038525100305,0.0570283675998011,9.70389517143639,0.0571487808577518,-1.2118566463360834,0.0807354808286009,-0.10860000000000002 +14 docked,12 docked,1.189428552203597,0.06352724768998895,5.133561828079143,0.06550814125922187,-3.9441332758755454,0.09125254939070675,2.257670000000001 +14 docked,13 docked,2.211090342537803,0.0627611295259399,5.344659118510516,0.06241161534550305,-3.1335687759727135,0.08851084176193805,0.9492500000000005 +16 docked,17 torsion adjust,5.730880014200166,0.04231414374496165,6.211918012734093,0.04289469238816712,-0.4810379985339263,0.06025314428264105,1.4577000000000002 +16 docked,19,-3.1158473773278867,0.038347429750655436,-2.7365326059936206,0.040926568629539924,-0.3793147713342662,0.05608484098461807,1.532200000000001 +17 torsion adjust,15 docked,-7.879821814925774,0.060130836765774846,-8.199561885517019,0.05825292866761249,0.31974007059124543,0.08372049467428037,0.28010000000000046 +18 docked,13 docked,-5.089113572008522,0.05639360091155245,-4.5607648808816705,0.055721207477216046,-0.5283486911268515,0.07927856700578288,-0.3712699999999998 +18 docked,15 docked,-10.827165506287551,0.053894350504713646,-11.39171648554417,0.0544376260839136,0.5645509792566201,0.07660323850841372,-0.49421999999999944 +18 docked,19,-11.09072770196693,0.034345473913258776,-11.953669928503386,0.03587461286613181,0.8629422265364555,0.04966487115276923,-0.6998199999999991 +19,17 torsion adjust,7.492563487501781,0.04589404906761103,9.078705770170902,0.0479540417335916,-1.586142282669122,0.06637660625858581,-0.0745000000000007 +20,11 docked,-4.67574345049406,0.07001706227998326,-5.209991195698426,0.06882046464562665,0.5342477452043664,0.0981766029375584,-0.8964000000000003 +20,15 docked,-15.969057201238716,0.05991774992754093,-16.500866557012827,0.06022330926605183,0.5318093557741106,0.08495283241501637,0.03850000000000058 +21 (Xtal),14 docked,1.9176954925126244,0.06377538853021053,0.12275843181152578,0.0625160719038044,1.7949370607010984,0.08930598764058853,2.1984999999999997 +21 (Xtal),16 docked,1.4917773405346142,0.05539038637762636,0.28996799911769644,0.053554125682151954,1.2018093414169178,0.07704634501806341,1.287 +21 (Xtal),22,-1.0396698663084876,0.04524486117024136,-1.1735377354779266,0.04420619256004125,0.13386786916943905,0.06325571059572298,0.0 +22,14 docked,3.5329097288990243,0.06847706421945333,1.2144742049155208,0.06668362981601722,2.3184355239835033,0.09558145641051279,2.1984999999999997 +22,16 docked,2.5833958498133818,0.0605708838342499,1.633343873772345,0.06082089541630932,0.9500519760410369,0.08583713233620886,1.287 +24 pose 2,14 docked,-1.9962060090197424,0.06611771026074198,-12.40530218591437,0.0644890476381553,10.409096176894629,0.09236010434922477,2.3072 +24 pose 2,16 docked,-2.714616215636306,0.0758646956996404,-12.285060389889715,0.07503393691799172,9.570444174253408,0.1067030634190612,1.3957000000000002 +24 pose 2,20,9.961744796019898,0.053376617673901235,2.4409618161834707,0.054534915555153114,7.5207829798364285,0.07630937248407633,3.095 diff --git a/summaries/jan_14_2026/water_set/chk1/dg_comparison_plot.png b/summaries/jan_14_2026/water_set/chk1/dg_comparison_plot.png new file mode 100644 index 0000000..cb565c8 Binary files /dev/null and b/summaries/jan_14_2026/water_set/chk1/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/water_set/chk1/dg_plot.png b/summaries/jan_14_2026/water_set/chk1/dg_plot.png new file mode 100644 index 0000000..586b119 Binary files /dev/null and b/summaries/jan_14_2026/water_set/chk1/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/chk1/dg_results.csv b/summaries/jan_14_2026/water_set/chk1/dg_results.csv new file mode 100644 index 0000000..7d47e53 --- /dev/null +++ b/summaries/jan_14_2026/water_set/chk1/dg_results.csv @@ -0,0 +1,14 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12 docked,Cn1cc(-c2ccc3c(-c4cc5cc(C[NH+]6CCOCC6)ccc5[nH]4)n[nH]c3c2)cn1,-12.248419095195066,0.05456982154328662,-8.61243 +11 docked,c1cc2[nH]c(-c3n[nH]c4cc(-c5cn[nH]c5)ccc34)cc2cc1C[NH+]1CCCCC1,-9.680103269084267,0.05405358973366299,-10.9787 +13 docked,c1cc(-c2ccc3c(-c4cc5cc(C[NH+]6CCOCC6)ccc5[nH]4)n[nH]c3c2)[nH]n1,-11.351139943811438,0.04449422147861768,-9.92085 +14 docked,c1cc2[nH]c(-c3n[nH]c4cc(-c5cnsc5)ccc34)cc2cc1C[NH+]1CCCCC1,-8.331311771855255,0.04224581757695513,-10.8701 +16 docked,c1cn(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)nn1,-9.4211945266314,0.036940919070656816,-11.7816 +17 torsion adjust,Cc1cnnn1-c1ccc2c(-c3cc4cc(C[NH+]5CCCCC5)ccc4[nH]3)n[nH]c2c1,-10.433680829719846,0.04739502080693951,-10.3239 +19,c1cnn(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)n1,-9.518657810726127,0.0432368285811125,-10.2494 +15 docked,c1csc(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)n1,-10.072322293121909,0.04672097075899792,-10.0438 +18 docked,c1cnn(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)c1,-10.536305270911333,0.04089603087617948,-9.54958 +20,c1ccc(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)cc1,-10.684965156597023,0.04906688937858691,-10.0823 +21 (Xtal),OCc1nn[nH]c1-c1ccc2c(-c3cc4cc(C[NH+]5CCCCC5)ccc4[nH]3)n[nH]c2c1,-10.475767233943472,0.05027700203032578,-13.0686 +22,OCc1nn[nH]c1-c1ccc2c(-c3cc4cc(C[N@H+]5CC[C@H](F)CC5)ccc4[nH]3)n[nH]c2c1,-10.418004810156763,0.0494764140589549,-13.0686 +24 pose 2,COc1cc(-c2ccc3c(-c4cc5cc(C[NH+]6CCCCC6)ccc5[nH]4)n[nH]c3c2)ccc1O,-18.555287988246082,0.050303986856296404,-13.1773 diff --git a/summaries/jan_14_2026/water_set/hsp90_kung/README.md b/summaries/jan_14_2026/water_set/hsp90_kung/README.md new file mode 100644 index 0000000..5721b37 --- /dev/null +++ b/summaries/jan_14_2026/water_set/hsp90_kung/README.md @@ -0,0 +1,39 @@ +# Hsp90 Kung Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.48 +- RMSE: 1.97 +- R²: 0.54 +- Kendall 𝜏: 0.56 +- Spearman ρ: 0.72 + +## System Details +- Ligands: 11 +- Host Atoms: 3432 +- Map Details: + - Edges: 18 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.6 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.45 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 1585.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/hsp90_kung/ddg_results.csv b/summaries/jan_14_2026/water_set/hsp90_kung/ddg_results.csv new file mode 100644 index 0000000..31c29be --- /dev/null +++ b/summaries/jan_14_2026/water_set/hsp90_kung/ddg_results.csv @@ -0,0 +1,19 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +cmpd 11,cmpd 10,-0.058109556059423646,0.047015590281091285,-0.6547571178743123,0.044869715461887276,0.5966475618148886,0.06499043848990535,0.0 +cmpd 11,cmpd 8,-13.614010307840129,0.06510839463123519,-21.40825504492421,0.06203914412671101,7.794244737084081,0.08993307764905789,2.3299999999999996 +cmpd 12,cmpd 10,-0.08063966188039884,0.04813179838869819,-1.3047393129270497,0.048055688462533615,1.2240996510466509,0.06801484550992067,0.0 +cmpd 12,cmpd 8,-13.833626387218418,0.06664151272775856,-22.426485378211275,0.0632085670787867,8.592858990992857,0.09184995465865775,2.3299999999999996 +cmpd 13,cmpd 10,6.391975141952973,0.058284562908215716,3.884198302816111,0.059101542552916574,2.507776839136862,0.08300652146389441,0.9600000000000005 +cmpd 13,cmpd 12,3.1348982211090015,0.045329670589599635,2.7807741419196566,0.04624422935533765,0.3541240791893453,0.06475575483639032,0.9600000000000005 +cmpd 14,cmpd 17,-4.1473352630658304,0.05551268585074986,-1.7065027233194199,0.052964298003312524,-2.4408325397464106,0.07672597443726432,-2.9199999999999986 +cmpd 15,cmpd 11,-0.6529335678720902,0.05498806282791714,-0.9875584200617455,0.05227887196525424,0.3346248521896553,0.07587336494137062,0.41999999999999865 +cmpd 15,cmpd 12,-0.20543526563053238,0.043981262790543235,-0.27739243950958187,0.04249773059078527,0.07195717387904947,0.0611588798296518,0.41999999999999865 +cmpd 15,cmpd 17,-1.5127711313273708,0.05466772016292015,-0.531429377813667,0.05399362001841525,-0.9813417535137039,0.07683664900621551,-1.130000000000001 +cmpd 16,cmpd 14,4.313789652660982,0.047641567760240616,2.7345809159792047,0.044476214125112844,1.579208736681777,0.06517555217684377,2.5099999999999985 +cmpd 16,cmpd 15,1.6118257264084241,0.04923224870466493,1.6851098963917843,0.044431313272829176,-0.07328416998336018,0.06631708612164942,0.7200000000000009 +cmpd 16,cmpd 17,0.374338933029178,0.042369721432356476,0.9675205074998595,0.0404594146957325,-0.5931815744706815,0.058584618559624865,-0.4100000000000002 +cmpd 7,cmpd 11,53.42810410496944,0.06321181829704177,57.94469825943399,0.06177162806364665,-4.516594154464548,0.08838250961616627,0.21999999999999945 +cmpd 7,cmpd 8,39.09971541322016,0.04158997101307736,36.74874473686662,0.03916875733550882,2.3509706763535396,0.0571307031295484,2.549999999999999 +cmpd 9,cmpd 13,-8.020943257029616,0.0458835463027285,-4.522222110360088,0.04571882108674986,-3.498721146669527,0.06477275988312428,-2.23 +cmpd 9,cmpd 14,-0.5609400996083,0.044753520651290665,-0.310136358114359,0.042283250137824614,-0.250803741493941,0.06156907383502975,0.0999999999999996 +cmpd 9,cmpd 7,-57.55634709577652,0.061940453091707086,-60.175039656517214,0.061913689215940836,2.618692560740693,0.08757810594854215,-1.4899999999999989 diff --git a/summaries/jan_14_2026/water_set/hsp90_kung/dg_comparison_plot.png b/summaries/jan_14_2026/water_set/hsp90_kung/dg_comparison_plot.png new file mode 100644 index 0000000..dbe5dab Binary files /dev/null and b/summaries/jan_14_2026/water_set/hsp90_kung/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/water_set/hsp90_kung/dg_plot.png b/summaries/jan_14_2026/water_set/hsp90_kung/dg_plot.png new file mode 100644 index 0000000..e0d371b Binary files /dev/null and b/summaries/jan_14_2026/water_set/hsp90_kung/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/hsp90_kung/dg_results.csv b/summaries/jan_14_2026/water_set/hsp90_kung/dg_results.csv new file mode 100644 index 0000000..278315d --- /dev/null +++ b/summaries/jan_14_2026/water_set/hsp90_kung/dg_results.csv @@ -0,0 +1,12 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 11,COc1cc(-c2nc(C)nc3[nH]cc(F)c23)c(Cl)cc1Cl,-10.244842179520829,0.038735334811548436,-9.19 +cmpd 10,COc1cc(-c2nc(C)nc3[nH]cc(C(C)=O)c23)c(Cl)cc1Cl,-9.572911421312458,0.04335977009816791,-9.19 +cmpd 8,COc1cc(-c2cc(C)nc(N)c2)c(Cl)cc1Cl,-2.762427913069936,0.043889846375237615,-6.86 +cmpd 12,COc1cc(-c2nc(C)nc3[nH]cc(Cl)c23)c(Cl)cc1Cl,-10.978389158907392,0.03435822341468123,-9.19 +cmpd 13,COc1cc(-c2nc(C)nc3[nH]cc(C#N)c23)c(Cl)cc1Cl,-11.687733107712008,0.0413993674662331,-10.15 +cmpd 14,COc1cc(-c2nc(C)nc3[nH]c(C)cc23)c(Cl)cc1Cl,-8.809827785476687,0.04211009969864757,-7.820000000000001 +cmpd 17,CCc1[nH]c2nc(C)nc(-c3cc(OC)c(Cl)cc3Cl)c2c1C#N,-11.345607313886116,0.048226857419072296,-10.74 +cmpd 15,COc1cc(-c2nc(C)nc3[nH]c(C)c(Cl)c23)c(Cl)cc1Cl,-10.713043747958096,0.03748420456371673,-9.61 +cmpd 16,COc1cc(-c2nc(C)nc3[nH]c(C)c(C#N)c23)c(Cl)cc1Cl,-10.605022804104529,0.04220383078083447,-10.33 +cmpd 7,COc1cc(-c2cc(C)nc(N)n2)c(Cl)cc1Cl,-5.385054475611387,0.045588335264017274,-9.41 +cmpd 9,COc1cc(-c2nc(C)nc3[nH]ccc23)c(Cl)cc1Cl,-8.305140092440558,0.04045739442236151,-7.920000000000001 diff --git a/summaries/jan_14_2026/water_set/hsp90_woodhead/README.md b/summaries/jan_14_2026/water_set/hsp90_woodhead/README.md new file mode 100644 index 0000000..b7443b7 --- /dev/null +++ b/summaries/jan_14_2026/water_set/hsp90_woodhead/README.md @@ -0,0 +1,39 @@ +# Hsp90 Woodhead Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.32 +- RMSE: 1.39 +- R²: 0.43 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.60 + +## System Details +- Ligands: 4 +- Host Atoms: 3268 +- Map Details: + - Edges: 6 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 5.3 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.38 Hours +- Average Time Per Edge: 0.23 Hours +- Total Nanoseconds Simulated: 618.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/hsp90_woodhead/ddg_results.csv b/summaries/jan_14_2026/water_set/hsp90_woodhead/ddg_results.csv new file mode 100644 index 0000000..7b6fadf --- /dev/null +++ b/summaries/jan_14_2026/water_set/hsp90_woodhead/ddg_results.csv @@ -0,0 +1,7 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +1,2,9.070073361999434,0.04518808278010123,10.516304056963321,0.04554179063329027,-1.4462306949638872,0.06415619626682778,1.9800000000000002 +1,3,22.54594219166237,0.059895082681561844,20.608708333446387,0.06065085300394705,1.937233858215982,0.08524052381078803,4.640000000000001 +3,2,-12.755758155853885,0.06239752859483013,-9.775551693621717,0.061841942847102115,-2.9802064622321685,0.08785145115390462,-2.6600000000000006 +4,1,-24.931175535632246,0.06130845174726783,-22.742299666513837,0.061883733771461544,-2.18887586911841,0.08711097956712573,-3.79 +4,2,-16.010281070433475,0.06466751732261747,-12.300205532200483,0.06505693517775238,-3.710075538232993,0.09172945334729356,-1.8099999999999996 +4,3,-3.6134186298437965,0.0374100808628539,-2.3491615924360887,0.03968439696746518,-1.2642570374077076,0.054537743928738266,0.8500000000000009 diff --git a/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_comparison_plot.png b/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_comparison_plot.png new file mode 100644 index 0000000..39d67ce Binary files /dev/null and b/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_plot.png b/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_plot.png new file mode 100644 index 0000000..133b200 Binary files /dev/null and b/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_results.csv b/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_results.csv new file mode 100644 index 0000000..cdd36cc --- /dev/null +++ b/summaries/jan_14_2026/water_set/hsp90_woodhead/dg_results.csv @@ -0,0 +1,5 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1,CC(C)c1cc(C(=O)N2Cc3ccccc3C2)c(O)cc1O,-10.780209488647767,0.03808487909256688,-12.72 +2,COc1cc(O)c(C(=O)N2Cc3ccccc3C2)cc1C(C)C,-12.168821778375328,0.03200890514383794,-10.74 +3,CC1(C)COc2cc(O)c(C(=O)N3Cc4ccccc4C3)cc21,-9.28397475068151,0.02800903626584409,-8.08 +4,CC1(C)CNc2cc(O)c(C(=O)N3Cc4ccccc4C3)cc21,-8.236993982295392,0.031096470933160848,-8.93 diff --git a/summaries/jan_14_2026/water_set/scyt_dehyd/README.md b/summaries/jan_14_2026/water_set/scyt_dehyd/README.md new file mode 100644 index 0000000..b6cff1d --- /dev/null +++ b/summaries/jan_14_2026/water_set/scyt_dehyd/README.md @@ -0,0 +1,39 @@ +# Scyt Dehyd Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.33 +- RMSE: 1.83 +- R²: 0.68 +- Kendall 𝜏: 0.52 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 7 +- Host Atoms: 2655 +- Map Details: + - Edges: 11 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 3 + - Mean Dummy Atoms: 1.8 + - Median Dummy Atoms: 2.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.52 Hours +- Average Time Per Edge: 0.14 Hours +- Total Nanoseconds Simulated: 747.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/scyt_dehyd/ddg_results.csv b/summaries/jan_14_2026/water_set/scyt_dehyd/ddg_results.csv new file mode 100644 index 0000000..1dda0bf --- /dev/null +++ b/summaries/jan_14_2026/water_set/scyt_dehyd/ddg_results.csv @@ -0,0 +1,12 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +2d,4d,27.409357857725325,0.051577919362568045,32.84454968728824,0.04988513572103349,-5.435191829562915,0.07175519863868751,-1.8617000000000024 +2d,7d,44.479447232311095,0.05744087921194742,52.74155228345916,0.05269132262300177,-8.262105051148064,0.07794761115263758,-1.7698000000000005 +3d,4d,-5.175224388785445,0.052020703360291964,1.5376439664101813,0.04888024087471529,-6.712868355195626,0.07138229140388867,-6.1501300000000025 +3d,5d,-19.155934432551035,0.04768037731343914,-14.551602531903054,0.04354593307866008,-4.6043319006479795,0.06457295616930561,-4.060230000000002 +3d,6d,11.137594026212518,0.03970453158882563,14.292379570828137,0.03865639286818985,-3.1547855446156183,0.055414497545930086,-0.21257999999999927 +4d,7d,16.640509163076413,0.042183046071193525,19.422090964635142,0.039888958336077064,-2.781581801558729,0.05805633792258798,0.091900000000002 +5d,6d,30.76185683327162,0.03857367297998057,28.573767169804626,0.03895612112469878,2.1880896634669926,0.05482251016004909,3.847650000000002 +5d,7d,29.902488230928842,0.05179639702372456,35.3580138534044,0.04890452540579865,-5.455525622475562,0.07123566066097589,-1.9979999999999993 +8d,2d,-38.00805719460192,0.0439935467211785,-38.004050691087144,0.043897059073310686,-0.0040065035147749065,0.06214808081022489,-2.8533 +8d,5d,-23.531205711037416,0.039168082751873216,-20.812702285716565,0.03902569509713402,-2.71850342532085,0.05529144223360482,-2.625100000000001 +8d,6d,7.82061750068109,0.04364114879821802,7.733420583883303,0.046027702839623603,0.08719691679778728,0.06342790629621083,1.2225500000000011 diff --git a/summaries/jan_14_2026/water_set/scyt_dehyd/dg_comparison_plot.png b/summaries/jan_14_2026/water_set/scyt_dehyd/dg_comparison_plot.png new file mode 100644 index 0000000..adb6a52 Binary files /dev/null and b/summaries/jan_14_2026/water_set/scyt_dehyd/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/water_set/scyt_dehyd/dg_plot.png b/summaries/jan_14_2026/water_set/scyt_dehyd/dg_plot.png new file mode 100644 index 0000000..f5a7211 Binary files /dev/null and b/summaries/jan_14_2026/water_set/scyt_dehyd/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/scyt_dehyd/dg_results.csv b/summaries/jan_14_2026/water_set/scyt_dehyd/dg_results.csv new file mode 100644 index 0000000..ea7681c --- /dev/null +++ b/summaries/jan_14_2026/water_set/scyt_dehyd/dg_results.csv @@ -0,0 +1,8 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2d,c1ccc(C(CCNc2ncnc3ccccc23)c2ccccc2)cc1,-10.21310077190058,0.04285425800327527,-13.4817 +4d,N#Cc1cnc2ccccc2c1NCCC(c1ccccc1)c1ccccc1,-15.401180449842174,0.03168955687799439,-15.343400000000003 +7d,N#Cc1nnc2ccccc2c1NCCC(c1ccccc1)c1ccccc1,-18.34417705221441,0.03490678862583734,-15.2515 +3d,c1ccc(C(CCNc2ccnc3ccccc23)c2ccccc2)cc1,-8.199741931769863,0.034431234536944404,-9.19327 +5d,c1ccc(C(CCNc2nnnc3ccccc23)c2ccccc2)cc1,-13.022234809996636,0.028151800779723183,-13.2535 +6d,c1ccc(C(CCNc2cnnc3ccccc23)c2ccccc2)cc1,-10.899424752295259,0.03138373982031263,-9.40585 +8d,c1ccc(C(CCNc2nncc3ccccc23)c2ccccc2)cc1,-10.47776023198107,0.03138000262202911,-10.6284 diff --git a/summaries/jan_14_2026/water_set/taf12/README.md b/summaries/jan_14_2026/water_set/taf12/README.md new file mode 100644 index 0000000..7782d85 --- /dev/null +++ b/summaries/jan_14_2026/water_set/taf12/README.md @@ -0,0 +1,39 @@ +# Taf12 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.73 +- RMSE: 0.88 +- R²: 0.02 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.14 + +## System Details +- Ligands: 8 +- Host Atoms: 2177 +- Map Details: + - Edges: 13 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 8 + - Mean Dummy Atoms: 4.2 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 2.03 Hours +- Average Time Per Edge: 0.16 Hours +- Total Nanoseconds Simulated: 978.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/taf12/ddg_results.csv b/summaries/jan_14_2026/water_set/taf12/ddg_results.csv new file mode 100644 index 0000000..09b926a --- /dev/null +++ b/summaries/jan_14_2026/water_set/taf12/ddg_results.csv @@ -0,0 +1,14 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +cmpd 2 (methyl),cmpd 3 (Allyl),2.8816756382477,0.05059582622619528,3.6113047010324584,0.04887826306477459,-0.7296290627847584,0.07034928735773134,1.5199999999999994 +cmpd 2 (methyl),cmpd 6 (ethyl),3.1842033843977373,0.0458437474005814,2.728173492072075,0.04252449763094644,0.45602989232566216,0.06252984946801553,1.3299999999999985 +cmpd 2 (methyl),cmpd 7 (n-propyl),4.416254576313884,0.04884023261808423,4.575270745255647,0.04579587298431671,-0.15901616894176385,0.06695244808507189,1.7399999999999987 +cmpd 3 (Allyl),cmpd 4 (Crotyl),3.654994504090906,0.04306142672763433,4.4286215750466065,0.039520475773109874,-0.7736270709557003,0.05844787829470275,-0.3700000000000014 +cmpd 3 (Allyl),cmpd 6 (ethyl),1.9559983455920942,0.046913128485470634,1.2536415890721464,0.04846699564993531,0.7023567565199478,0.06745288201126119,-0.19000000000000075 +cmpd 3 (Allyl),cmpd 8 (n-Butyl),12.073706301559055,0.0565457368491309,12.559665916410754,0.056084060813746256,-0.48595961485169864,0.07964196276568747,0.060000000000000775 +cmpd 5 (1-Butenyl),cmpd 7 (n-propyl),0.7113467937133147,0.045459034691538974,-0.12670580019217728,0.04503010759149161,0.838052593905492,0.06398620495691125,1.8800000000000006 +cmpd 5 (1-Butenyl),cmpd 8 (n-Butyl),9.213903921478824,0.051415193556274684,8.69364882868774,0.05329627955072933,0.5202550927910833,0.07405413926566616,1.720000000000002 +cmpd 5 (1-Butenyl),cmpd 9 (methoxyethyl),-4.4021239196521185,0.04784438253665957,-5.333964489150322,0.04875373063531016,0.931840569498203,0.06830820734856534,2.309999999999999 +cmpd 6 (ethyl),cmpd 7 (n-propyl),1.914200984915249,0.04167407321201207,2.529003964018169,0.04098408976273705,-0.61480297910292,0.05845018384710376,0.4100000000000002 +cmpd 8 (n-Butyl),cmpd 4 (Crotyl),-9.651235190049599,0.05507495710161516,-9.2168621487953,0.05492779886641841,-0.43437304125429727,0.07778376429599217,-0.43000000000000216 +cmpd 9 (methoxyethyl),cmpd 4 (Crotyl),5.112213330221651,0.05238029650938927,4.808221806687907,0.05333224440000584,0.30399152353374326,0.07475308525508156,-1.0199999999999996 +cmpd 9 (methoxyethyl),cmpd 8 (n-Butyl),12.123211536638875,0.040679644075293946,12.154016064055483,0.04084871244986063,-0.030804527416608215,0.05764937771480275,-0.5899999999999974 diff --git a/summaries/jan_14_2026/water_set/taf12/dg_plot.png b/summaries/jan_14_2026/water_set/taf12/dg_plot.png new file mode 100644 index 0000000..9e62abe Binary files /dev/null and b/summaries/jan_14_2026/water_set/taf12/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/taf12/dg_results.csv b/summaries/jan_14_2026/water_set/taf12/dg_results.csv new file mode 100644 index 0000000..f3b4a47 --- /dev/null +++ b/summaries/jan_14_2026/water_set/taf12/dg_results.csv @@ -0,0 +1,9 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +cmpd 2 (methyl),CN(C)C(=O)c1cccc(-c2cn(C)c(=O)c3[nH]ccc23)c1,-8.13599075714996,0.04069163516697785,-9.86 +cmpd 3 (Allyl),C=CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.53199849705265,0.03314154739638979,-8.34 +cmpd 6 (ethyl),CCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-7.7899594683332065,0.04031014216076179,-8.53 +cmpd 7 (n-propyl),CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.471079259156893,0.0386250604223193,-8.12 +cmpd 4 (Crotyl),C/C=C/Cn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.143155136662415,0.03874842457284893,-8.71 +cmpd 8 (n-Butyl),CCCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.947358948276936,0.034169029974187685,-8.28 +cmpd 5 (1-Butenyl),C=CCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-9.549422372823864,0.042313847940177375,-10.0 +cmpd 9 (methoxyethyl),COCCn1cc(-c2cccc(C(=O)N(C)C)c2)c2cc[nH]c2c1=O,-8.961035560544076,0.041731611933562285,-7.690000000000001 diff --git a/summaries/jan_14_2026/water_set/urokinase/README.md b/summaries/jan_14_2026/water_set/urokinase/README.md new file mode 100644 index 0000000..836ebef --- /dev/null +++ b/summaries/jan_14_2026/water_set/urokinase/README.md @@ -0,0 +1,39 @@ +# Urokinase Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.68 +- RMSE: 0.70 +- R²: 0.56 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.80 + +## System Details +- Ligands: 4 +- Host Atoms: 4017 +- Map Details: + - Edges: 6 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 3 + - Mean Dummy Atoms: 1.8 + - Median Dummy Atoms: 2.0 + +## Simulation Details +- TMD Sha: [be54a617e0ca39fba04baa293394cc65f12327f5](https://github.com/tmd-industries/tmd/tree/be54a617e0ca39fba04baa293394cc65f12327f5) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 1.00 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 435.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 614943 + - Equilibration Steps: 200000 + - Steps Per Frame: 400 + - Production Ns: 2 + - Target Overlap: 0.667 + - Water Sampling: True + - REST: Temperature Scale 3.0 + - Local MD: Steps 390, Radius 1.2 diff --git a/summaries/jan_14_2026/water_set/urokinase/ddg_results.csv b/summaries/jan_14_2026/water_set/urokinase/ddg_results.csv new file mode 100644 index 0000000..47cb723 --- /dev/null +++ b/summaries/jan_14_2026/water_set/urokinase/ddg_results.csv @@ -0,0 +1,7 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +"10302 (1GJ7, no water pose)",11417 (no water pose),2.131107659392933,0.04431279010214106,0.4794386298256035,0.04345320035597094,1.6516690295673293,0.06206290347552686,0.25679999999999964 +"10302 (1GJ7, no water pose)",7806 (no water pose),-10.675220590211671,0.05119961060875757,-12.862918460566158,0.05368686778549593,2.1876978703544885,0.07418679059715229,2.1708999999999996 +"10302 (1GJ7, no water pose)",8696 (no water pose),1.9246419431573287,0.042622618155620975,-0.9724937275186804,0.042402353856294914,2.897135670676009,0.060121936021674476,1.0202299999999995 +11417 (no water pose),7806 (no water pose),-11.92918586422919,0.051922768483052203,-12.911130793714488,0.052110803534266406,0.9819449294852981,0.0735629644041861,1.9141 +11417 (no water pose),8696 (no water pose),-0.12956563444976185,0.04016388888683143,-0.821900630033161,0.04298447438070434,0.6923349955833992,0.058828590058739035,0.7634299999999998 +7806 (no water pose),8696 (no water pose),12.031861328831575,0.04420560926127781,11.998148417831015,0.04486657899661018,0.03371291100056111,0.06298528241597265,-1.15067 diff --git a/summaries/jan_14_2026/water_set/urokinase/dg_comparison_plot.png b/summaries/jan_14_2026/water_set/urokinase/dg_comparison_plot.png new file mode 100644 index 0000000..1cb1b7c Binary files /dev/null and b/summaries/jan_14_2026/water_set/urokinase/dg_comparison_plot.png differ diff --git a/summaries/jan_14_2026/water_set/urokinase/dg_plot.png b/summaries/jan_14_2026/water_set/urokinase/dg_plot.png new file mode 100644 index 0000000..ee79dec Binary files /dev/null and b/summaries/jan_14_2026/water_set/urokinase/dg_plot.png differ diff --git a/summaries/jan_14_2026/water_set/urokinase/dg_results.csv b/summaries/jan_14_2026/water_set/urokinase/dg_results.csv new file mode 100644 index 0000000..a27a74e --- /dev/null +++ b/summaries/jan_14_2026/water_set/urokinase/dg_results.csv @@ -0,0 +1,5 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +"10302 (1GJ7, no water pose)",NC(=[NH2+])c1cc2cc(-c3cccc(-c4ccccc4)c3[O-])[nH]c2cc1Cl,-11.672934911071666,0.027364758398047334,-10.8224 +11417 (no water pose),NC(=[NH2+])c1cc2cc(-c3cccc(-c4ccccc4)c3[O-])[nH]c2cc1F,-9.945762064890314,0.028398553512486907,-10.5656 +7806 (no water pose),NC(=[NH2+])c1ccc2[nH]c(-c3cccc(-c4ccccc4)c3[O-])nc2c1,-9.167904607338896,0.026280693312731626,-8.6515 +8696 (no water pose),NC(=[NH2+])c1ccc2[nH]c(-c3cccc(-c4ccccc4)c3[O-])cc2c1,-9.055068416699118,0.025261339980652615,-9.80217