diff --git a/summaries/dec_09_2025/README.md b/summaries/dec_09_2025/README.md new file mode 100644 index 0000000..7f03bf4 --- /dev/null +++ b/summaries/dec_09_2025/README.md @@ -0,0 +1,15 @@ +# Summary Dec 09 2025 +- Number of Datasets: 19 +- Number of Ligands: 476 +- Number of Edges: 843 +- Total Wallclock Time: 109.24 Hours +- Average Time Per Edge: 0.13 Hours +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) + +![Retrospective dG performance](dg_plot.png) + +## Notes: +- Adds an aggregate plot to the summary. Don't read into these plots, the per target performance is what matters +- Adds comparison plots for each set against the the results of the Dec 08 2025 run, which used OpenFF 2.2.1. +- Repeat of December 8th summary, but with OpenFF 2.0.0 and run on a machine with a RTX 5090 and RTX 5080 +- Hif2a Ligand 35 still has an incorrect experimental [label](https://chemrxiv.org/engage/chemrxiv/article-details/65281c688bab5d205536cc7b). diff --git a/summaries/dec_09_2025/dg_plot.png b/summaries/dec_09_2025/dg_plot.png new file mode 100644 index 0000000..7bd3a16 Binary files /dev/null and b/summaries/dec_09_2025/dg_plot.png differ diff --git a/summaries/dec_09_2025/jacs/cdk2/README.md b/summaries/dec_09_2025/jacs/cdk2/README.md new file mode 100644 index 0000000..a786118 --- /dev/null +++ b/summaries/dec_09_2025/jacs/cdk2/README.md @@ -0,0 +1,38 @@ +# Cdk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.70 +- RMSE: 0.89 +- R²: 0.70 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.83 + +## System Details +- Ligands: 16 +- Host Atoms: 4825 +- Map Details: + - Edges: 29 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 11 + - Mean Dummy Atoms: 4.5 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 3.47 Hours +- Total Nanoseconds Simulated: 3549.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/jacs/cdk2/ddg_results.csv b/summaries/dec_09_2025/jacs/cdk2/ddg_results.csv new file mode 100644 index 0000000..13e9b85 --- /dev/null +++ b/summaries/dec_09_2025/jacs/cdk2/ddg_results.csv @@ -0,0 +1,30 @@ +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) +17,1oiu,-61.46467892453873,0.04831895359814959,-58.24215208748517,0.04632132936372358,-3.2225268370535667,0.0669356917559137,-2.04 +17,20,-5.141454756239709,0.06815680504505664,-4.6236440294885774,0.0669081505346736,-0.5178107267511314,0.09550942718873567,-1.6800000000000006 +17,21,3.1299027741380305,0.06692047726080952,2.4274547634027055,0.06574192901958172,0.7024480107353248,0.09381018872185604,-0.7899999999999991 +17,26,2.051862466154019,0.0665680462743112,2.355117589713989,0.0664003037919182,-0.30325512355997025,0.0940228968307075,-1.3900000000000001 +1h1r,1h1q,2.6614117771770855,0.055295277744575294,1.3691512277780933,0.05432230281242264,1.2922605493989923,0.07751438784957451,-0.5099999999999998 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+1h1s,1oiy,36.355661508549595,0.06495032689496233,35.37792208290524,0.06424959484457617,0.9777394256443468,0.09135948446359937,1.4600000000000002 +1h1s,29,50.10026488403073,0.05990315448534542,47.51985202027057,0.060233776270748565,2.5804128637601615,0.08494996010081317,1.369999999999999 +1h1s,31,41.93603214008069,0.05589219806241611,40.458105815023785,0.05374566069164238,1.477926325056909,0.07754053035303217,1.71 +1h1s,32,11.377666163077583,0.053841414463502824,7.9897523185012504,0.049990431540099946,3.387913844576332,0.07347068229570289,1.4999999999999991 +1oiu,1h1q,63.02487465267697,0.06659864744797775,59.47380700170865,0.06591275095888197,3.551067650968319,0.09370096360693218,0.9000000000000015 +1oiy,31,1.2751900264620126,0.0677348184473766,0.21301254546037782,0.06877706397113786,1.0621774810016347,0.09653129108526964,0.24999999999999983 +21,20,-7.2989226660725155,0.052754348062902155,-6.440710582476848,0.0519485933065714,-0.8582120835956668,0.0740383521296455,-0.8900000000000013 +22,1h1q,-1.187380820704362,0.06316506361402169,0.23763057238884966,0.06050999882209375,-1.4250113930932116,0.0874716252210578,-0.31999999999999906 +22,1h1r,-4.018685036105246,0.07228776121532574,-1.2685340042442899,0.06830071170178663,-2.750151031860956,0.09945103136968728,0.19000000000000075 +22,32,-55.027377342828835,0.07287377524456015,-51.217658116775574,0.07194166679879824,-3.809719226053267,0.10240210222541321,-1.8900000000000008 +26,1oi9,-9.549530102175414,0.058584846292244,-9.088561729462642,0.05712628666420647,-0.4609683727127716,0.08182662673682052,-1.31 +28,1h1s,-22.77485518294535,0.0590302765830656,-23.506567530526187,0.05698429919258725,0.7317123475808389,0.08204744912514662,-0.14000000000000012 +28,1oiy,11.869174829429705,0.06832011505609249,11.307651601682814,0.06640733220360454,0.5615232277468918,0.0952762923904872,1.32 +28,30,17.12078305663577,0.055889729997829124,15.881026462045071,0.056237063568714905,1.2397565945906992,0.07928599648148418,1.2999999999999998 +29,1oi9,-5.621412278290615,0.07559849437467307,-6.247314158362024,0.07250713239417442,0.6259018800714092,0.10474930357641436,0.14000000000000012 +30,29,14.015953054091776,0.062142728651729956,13.876926992099778,0.06024872330393724,0.13902606199199813,0.08655418755922172,-0.07000000000000091 +30,31,3.9397406041848986,0.04841736252366757,2.66051305574073,0.04677807429768206,1.2792275484441682,0.06732331861062489,0.2700000000000001 +30,32,-30.80166514691511,0.05789829385374023,-30.566832781709973,0.058290330605524146,-0.23483236520513592,0.08215823192641962,0.05999999999999908 diff --git a/summaries/dec_09_2025/jacs/cdk2/dg_comparison_plot.png b/summaries/dec_09_2025/jacs/cdk2/dg_comparison_plot.png new file mode 100644 index 0000000..b3bc7e7 Binary files /dev/null and b/summaries/dec_09_2025/jacs/cdk2/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/jacs/cdk2/dg_plot.png b/summaries/dec_09_2025/jacs/cdk2/dg_plot.png new file mode 100644 index 0000000..073315c Binary files /dev/null and b/summaries/dec_09_2025/jacs/cdk2/dg_plot.png differ diff --git a/summaries/dec_09_2025/jacs/cdk2/dg_results.csv b/summaries/dec_09_2025/jacs/cdk2/dg_results.csv new file mode 100644 index 0000000..3767a10 --- /dev/null +++ b/summaries/dec_09_2025/jacs/cdk2/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17,Brc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.836119457012859,0.058638610140029516,-7.04 +1oiu,NS(=O)(=O)c1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-10.86340191746214,0.061177090634747223,-9.08 +20,OCc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.267680359658707,0.06579982200104406,-8.72 +21,COc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.362557079839101,0.05730179348009877,-7.829999999999999 +26,COc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.378274726392972,0.05591517173297361,-8.43 +1h1r,Clc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.620196288471277,0.043907200366213574,-7.669999999999999 +1h1q,c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-7.266036172571557,0.05708041023111441,-8.18 +1oi9,Oc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.212004760008341,0.04689814968614398,-9.74 +1h1s,NS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.588628165644918,0.05137621338902752,-11.25 +1oiy,NC(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-10.721205747685305,0.06418524889905178,-9.79 +29,CN(C)S(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.542148831190099,0.06508490624149531,-9.88 +31,C[S@](=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.40716138780068,0.05989605471499196,-9.54 +32,COc1cc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)ccc1S(N)(=O)=O,-9.211132100475796,0.049684591211010834,-9.75 +22,CSc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-5.7218541544611305,0.062411757414341115,-7.86 +28,CNS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.648068311141179,0.06438563755269504,-11.11 +30,CS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-10.033530540183927,0.055517229256799826,-9.81 diff --git a/summaries/dec_09_2025/jacs/mcl1/README.md b/summaries/dec_09_2025/jacs/mcl1/README.md new file mode 100644 index 0000000..43b7303 --- /dev/null +++ b/summaries/dec_09_2025/jacs/mcl1/README.md @@ -0,0 +1,38 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.48 +- RMSE: 1.81 +- R²: 0.17 +- Kendall 𝜏: 0.27 +- Spearman ρ: 0.39 + +## System Details +- Ligands: 69 +- Host Atoms: 2536 +- Map Details: + - Edges: 129 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 3.3 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 15.37 Hours +- Total Nanoseconds Simulated: 17045.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/jacs/mcl1/ddg_results.csv b/summaries/dec_09_2025/jacs/mcl1/ddg_results.csv new file mode 100644 index 0000000..c87199e --- /dev/null +++ b/summaries/dec_09_2025/jacs/mcl1/ddg_results.csv @@ -0,0 +1,130 @@ +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 flip,42 flip,5.472615706819211,0.054408838200574225,4.725854746832069,0.054556693822832146,0.7467609599871425,0.07705033754121078,-0.0699999999999992 +23 flip,44 flip,1.7199553321533685,0.06616521849910427,3.2389304082281893,0.06668440589300154,-1.5189750760748206,0.09393958765258015,0.16000000000000036 +23 flip,51 flip,7.2357372796666,0.06668198643417135,7.051541537414251,0.0654093045072507,0.18419574225234883,0.09340698277393002,0.3800000000000015 +23 flip,64 flip,-2.47129379302672,0.054135288613803664,-1.7042174239680283,0.05454596756539371,-0.7670763690586918,0.07684980189268419,-0.6700000000000002 +23 flip,66 flip,-2.002577887026196,0.05440452673710718,-0.6834248047724354,0.05480249866915584,-1.3191530822537607,0.07722154097058306,0.4000000000000001 +23 flip,68 flip,12.451458885249693,0.06277906696224052,13.17259207125304,0.0626268024041984,-0.7211331860033482,0.08867540599300344,1.1399999999999995 +23,42,5.632891053352943,0.05476929695040733,4.956419996369466,0.05667969436807251,0.6764710569834771,0.07881791447443919,-0.0699999999999992 +23,44,4.205140819817685,0.06656816045654973,3.6996791516776186,0.06671800909977045,0.5054616681400661,0.09424761389449605,0.16000000000000036 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flip,8.511943871293118,0.055299663740117445,5.9946429726765,0.05301389263974602,2.517300898616618,0.07660630276020752,-0.8200000000000004 +27,30 flip,0.6817316950244621,0.048720628031097876,0.6172009442526242,0.04758701615668105,0.06453075077183791,0.06810450574257788,-1.7299999999999995 +27,32,-0.15191604230026126,0.04897282927665639,0.5493075760241465,0.047449912308120026,-0.7012236183244078,0.06818967799754456,-0.46 +27,40,12.616062455684585,0.060409936045860514,16.593647477185275,0.05859900241664862,-3.977585021500691,0.08416176957081731,-1.1299999999999994 +27,41,17.15464917871728,0.060997769443787805,16.53096420713765,0.05871517825125807,0.6236849715796301,0.08466522328674567,-1.0099999999999996 +27,40 flip,15.391673208628605,0.059929081490102086,16.7009353820279,0.05910866915011932,-1.3092621733992948,0.0841743997718164,-1.1299999999999994 +27,41 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index 0000000..6171624 Binary files /dev/null and b/summaries/dec_09_2025/jacs/mcl1/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/jacs/mcl1/dg_plot.png b/summaries/dec_09_2025/jacs/mcl1/dg_plot.png new file mode 100644 index 0000000..ad54b6a Binary files /dev/null and b/summaries/dec_09_2025/jacs/mcl1/dg_plot.png differ diff --git a/summaries/dec_09_2025/jacs/mcl1/dg_results.csv b/summaries/dec_09_2025/jacs/mcl1/dg_results.csv new file mode 100644 index 0000000..1894720 --- /dev/null +++ b/summaries/dec_09_2025/jacs/mcl1/dg_results.csv @@ -0,0 +1,70 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +23 flip,O=C([O-])c1sc2ccccc2c1CCCOc1cccc2ccccc12,-5.786393352473921,0.08243549786882076,-8.83 +42 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2ccccc12,-5.046418598822411,0.0745250270350111,-8.9 +44 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-6.8318518004611555,0.09473016527455215,-8.67 +51 flip,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-6.060386854975669,0.08615558108448859,-8.45 +64 flip,O=C([O-])c1sc2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-6.5429301431499125,0.10831755667261538,-9.5 +66 flip,O=C([O-])c1sc2c(Cl)cccc2c1CCCOc1cccc2ccccc12,-7.134842007248003,0.10618651254876776,-8.43 +68 flip,O=C([O-])c1oc2ccc(Cl)cc2c1CCCOc1cccc2ccccc12,-6.482928755264062,0.11135230218315798,-7.690000000000001 +23,O=C([O-])c1sc2ccccc2c1CCCOc1cccc2ccccc12,-8.796110475568131,0.08201012359345289,-8.83 +42,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2ccccc12,-8.180337985467531,0.07633237877317905,-8.9 +44,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-8.348753425457948,0.08801317868091058,-8.67 +51,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-7.4349370570027,0.08391337713032192,-8.45 +64,O=C([O-])c1sc2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-10.298470883957,0.10050805539173079,-9.5 +66,O=C([O-])c1sc2c(Cl)cccc2c1CCCOc1cccc2ccccc12,-10.31764519788001,0.1068408797959279,-8.43 +68,O=C([O-])c1oc2ccc(Cl)cc2c1CCCOc1cccc2ccccc12,-7.896321607333237,0.09967827243309756,-7.690000000000001 +26 flip,O=C([O-])c1oc2ccccc2c1CCCOc1cccc2ccccc12,-6.174209848959035,0.11092458746591255,-8.24 +26,O=C([O-])c1oc2ccccc2c1CCCOc1cccc2ccccc12,-9.247501345919446,0.10956466627999649,-8.24 +27,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1,-7.1294052505871575,0.03919068848263848,-6.12 +28 flip,Cc1ccccc1OCCCc1c(C(=O)[O-])[nH]c2ccccc12,-4.873307628277366,0.06173065037342709,-6.62 +29,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1C(F)(F)F,-4.448465347888601,0.05321666709670922,-6.94 +29 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1C(F)(F)F,-4.922732880090227,0.056642078898501,-6.94 +30 flip,Cc1cccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)c1,-6.733386669871315,0.058750591881374256,-7.85 +32,Cc1ccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc1,-7.774381327048889,0.05457815092560537,-6.58 +40,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(Oc2ccccc2)c1,-10.537301455305606,0.05871232329207226,-7.25 +41,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Oc2ccccc2)cc1,-7.520991911638705,0.06359961604623815,-7.13 +40 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(Oc2ccccc2)c1,-8.419862484976537,0.06141130346684551,-7.25 +41 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Oc2ccccc2)cc1,-9.557976489105567,0.06556604059706324,-7.13 +48,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2[nH]ccc12,-4.236059126371069,0.059463754749036986,-6.66 +48 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2[nH]ccc12,-3.7484428211172727,0.06280678431704978,-6.66 +28,Cc1ccccc1OCCCc1c(C(=O)[O-])[nH]c2ccccc12,-5.994205280266923,0.06550271282523201,-6.62 +33,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)cc1,-7.790961720639846,0.04337840422208911,-6.88 +35 flip,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-7.776111031444668,0.0812414885661589,-8.81 +36 flip,CCc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-7.501172322424941,0.08282198022705653,-8.18 +38,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(-c2ccccc2)c1,-6.831394406701544,0.08949011899558255,-7.02 +43 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ccccc2c1,-7.150078931921559,0.07369225697470466,-7.03 +46 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2c(c1)CCC2,-7.228224260318769,0.08470512190131044,-7.6 +49 flip,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)ccc1Cl,-8.097008542388007,0.08189960986286142,-8.36 +52 flip,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)ccc1Cl,-9.783495334815797,0.08325305556058848,-9.23 +30,Cc1cccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)c1,-7.653771625113404,0.06776852479391517,-7.85 +36,CCc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-9.97488224815978,0.08158553698607168,-8.18 +37,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc(C)c1Cl,-9.490771404212872,0.09151318436789839,-8.95 +38 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(-c2ccccc2)c1,-11.295644167807076,0.08378920168509676,-7.02 +45,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2c1CCCC2,-9.328205733630172,0.09332947541548241,-8.95 +46,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2c(c1)CCC2,-9.185188013723875,0.08818589185445497,-7.6 +49,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)ccc1Cl,-8.862118334406937,0.09282530510027318,-8.36 +50,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)cc(C)c1Cl,-8.940856592253104,0.09221045522654382,-9.33 +52,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)ccc1Cl,-11.017513814263692,0.09118332413001715,-9.23 +53,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)cc(C)c1Cl,-11.121781959051022,0.09550344208222096,-9.96 +31 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(C(F)(F)F)c1,-7.155799479179724,0.07913075240101274,-7.920000000000001 +31,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(C(F)(F)F)c1,-9.130649688101764,0.09494491896481504,-7.920000000000001 +34,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(C(F)(F)F)cc1,-8.077122224161618,0.05841809894654152,-6.87 +39,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(-c2ccccc2)cc1,-8.351286840842514,0.07189397869494478,-7.03 +35,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-9.538419167655602,0.09506528788471617,-8.81 +56,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3ccccc23)cc(C)c1Cl,-10.628499629840096,0.09239863603438428,-9.26 +58,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3cc(Cl)ccc23)cc(C)c1Cl,-12.07391495774611,0.10524945499657024,-9.41 +60,Cc1cc(OCCCc2c(C(=O)[O-])sc3ccccc23)cc(C)c1Cl,-10.279240910710012,0.10485966005986033,-8.92 +63,Cc1cc(OCCCc2c(C(=O)[O-])sc3cc(Cl)ccc23)cc(C)c1Cl,-11.707241000796756,0.10766202058538574,-9.06 +47,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ncccc2c1,-7.092344688933731,0.08892299371653063,-5.78 +47 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ncccc2c1,-5.189116602895176,0.07266038385040752,-5.78 +43,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ccccc2c1,-8.624389508368505,0.07977978419929002,-7.03 +45 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2c1CCCC2,-5.8329530759032195,0.0812881518161656,-8.95 +54 flip,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-6.584167285442241,0.08599728031452317,-9.78 +57 flip,Cn1c(C(=O)[O-])c(CCCOc2cccc3ccccc23)c2ccccc21,-5.796103813056738,0.08556374921085387,-9.04 +54,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-10.18930265262301,0.08505147888893778,-9.78 +57,Cn1c(C(=O)[O-])c(CCCOc2cccc3ccccc23)c2ccccc21,-8.51363947732638,0.09713159861527372,-9.04 +61,Cc1cc(OCCCc2c(C(=O)[O-])sc3cccc(Cl)c23)cc(C)c1Cl,-9.459025102100567,0.11269762639600554,-8.08 +65,Cc1cc(OCCCc2c(C(=O)[O-])sc3c(Cl)cccc23)cc(C)c1Cl,-11.886795313884088,0.10778953251853256,-8.41 +67,Cc1cc(OCCCc2c(C(=O)[O-])oc3ccccc23)cc(C)c1Cl,-10.964454193071381,0.11766658074982957,-7.58 +62 flip,O=C([O-])c1sc2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-6.413912129440693,0.11910999465549747,-7.959999999999999 +62,O=C([O-])c1sc2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-7.085883802157507,0.10227167790907556,-7.959999999999999 diff --git a/summaries/dec_09_2025/jacs/p38/README.md b/summaries/dec_09_2025/jacs/p38/README.md new file mode 100644 index 0000000..931fc01 --- /dev/null +++ b/summaries/dec_09_2025/jacs/p38/README.md @@ -0,0 +1,38 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.95 +- RMSE: 1.19 +- R²: 0.41 +- Kendall 𝜏: 0.48 +- Spearman ρ: 0.67 + +## System Details +- Ligands: 34 +- Host Atoms: 6681 +- Map Details: + - Edges: 64 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 6.9 + - Median Dummy Atoms: 6.5 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 8.53 Hours +- Total Nanoseconds Simulated: 8836.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/jacs/p38/ddg_results.csv b/summaries/dec_09_2025/jacs/p38/ddg_results.csv new file mode 100644 index 0000000..9aaea4d --- /dev/null +++ b/summaries/dec_09_2025/jacs/p38/ddg_results.csv @@ -0,0 +1,65 @@ +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,2v,11.63605020322374,0.06349709477700353,11.490089936044988,0.06280309155023947,0.14596026717875002,0.08930906646801057,0.29999999999999877 +2aa,2y,13.089460226016609,0.0683927045951409,13.625805662081511,0.06897164870960781,-0.5363454360649029,0.09713212840023505,-0.5099999999999998 +2aa,2z,7.822909614430972,0.06711228106706292,8.582735476662235,0.06509022700735617,-0.7598258622312629,0.0934922238578889,-1.0900000000000005 +2aa,3flq,-6.98969832800226,0.07320253347467238,-6.076206546493442,0.07195210571827468,-0.9134917815088182,0.10264363801232061,-0.66 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+2o,CS(=O)(=O)CCn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-12.111568361907757,0.0682703460543887,-10.49 +2p,CS(=O)(=O)CCCn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-12.193344213027496,0.07612207840494055,-11.2 diff --git a/summaries/dec_09_2025/jacs/ptp1b/README.md b/summaries/dec_09_2025/jacs/ptp1b/README.md new file mode 100644 index 0000000..3d2a88a --- /dev/null +++ b/summaries/dec_09_2025/jacs/ptp1b/README.md @@ -0,0 +1,38 @@ +# Ptp1B Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.90 +- RMSE: 1.65 +- R²: 0.30 +- Kendall 𝜏: 0.54 +- Spearman ρ: 0.69 + +## System Details +- Ligands: 23 +- Host Atoms: 5488 +- Map Details: + - Edges: 39 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 24 + - Mean Dummy Atoms: 9.7 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 5.42 Hours +- Total Nanoseconds Simulated: 5645.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/jacs/ptp1b/ddg_results.csv b/summaries/dec_09_2025/jacs/ptp1b/ddg_results.csv new file mode 100644 index 0000000..bfd6a94 --- /dev/null +++ b/summaries/dec_09_2025/jacs/ptp1b/ddg_results.csv @@ -0,0 +1,40 @@ +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) +20667,23485,5.714122017717415,0.042635993563270684,3.6649542143387213,0.04322611974525552,2.0491678033786935,0.06071511653088074,0.4100000000000002 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b/summaries/dec_09_2025/jacs/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,-11.78308504608722,0.08700922610302897,-11.42 +23485,Cc1c(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc(C(=O)[O-])c1OCC(=O)[O-],-9.623344911267473,0.0905611709170868,-11.01 +23486,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Cl,-12.5994568260768,0.08386237613362714,-12.47 +20669,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCc3ccccc3)c2)c1Br,-7.907473448254122,0.07367927179005394,-8.61 +23466,Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-5.915811974414374,0.0739601078437056,-7.85 +23470,CC(C)NC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-8.15542784757614,0.06708544808008451,-7.72 +20670,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCC3)c2)c1Br,-8.427026203637853,0.06844872006217242,-9.08 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-0,0 +1,38 @@ +# Tyk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.54 +- RMSE: 0.71 +- R²: 0.68 +- Kendall 𝜏: 0.53 +- Spearman ρ: 0.75 + +## System Details +- Ligands: 16 +- Host Atoms: 4670 +- Map Details: + - Edges: 26 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 5.1 + - Median Dummy Atoms: 5.5 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 2.66 Hours +- Total Nanoseconds Simulated: 2817.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/jacs/tyk2/ddg_results.csv b/summaries/dec_09_2025/jacs/tyk2/ddg_results.csv new file mode 100644 index 0000000..457f4ce --- /dev/null +++ b/summaries/dec_09_2025/jacs/tyk2/ddg_results.csv @@ -0,0 +1,27 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +ejm_31,ejm_48,31.950912531798387,0.07082460325899913,31.85915146949434,0.0677892886398278,0.09176106230404832,0.0980383194525922,0.5400000000000001 +ejm_31,ejm_49,26.090902892624705,0.07258559280368718,24.32773534960234,0.06944017368480863,1.7631675430223677,0.100452008461947,1.7899999999999994 +ejm_31,ejm_50,-2.4030818068739395,0.04328893020122993,-2.30223375475127,0.043210741606500784,-0.10084805212266935,0.0611645294934142,0.5599999999999987 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+ejm_50,ejm_44,17.3203765416921,0.06307178557530382,14.779838451248157,0.06265179094629218,2.5405380904439427,0.08890048956240344,1.5600000000000007 +ejm_50,ejm_45,20.388827258602944,0.047387329123406624,19.777605480613982,0.04590193724932992,0.6112217779889609,0.06597383424276236,-0.5799999999999991 +ejm_50,ejm_55,2.2366273608101346,0.05443140285027229,2.342769535831854,0.053227411999123675,-0.10614217502171971,0.07613103837708432,-0.2299999999999996 +ejm_55,ejm_43,12.339544782819305,0.05150903992593949,10.521525902051467,0.05116983627858455,1.8180188807678381,0.07260532582992225,0.9500000000000004 +ejm_55,ejm_47,74.10770094668261,0.06792280039785724,73.64949779574991,0.06645783564920231,0.45820315093269537,0.09502710525457218,-0.48999999999999955 +jmc_27,jmc_23,-0.5238549677583492,0.04223003361509881,-0.5850647799482865,0.04394364211041212,0.06120981218993739,0.06094603695943126,-0.41999999999999865 +jmc_28,ejm_54,-48.995080840478664,0.06232096956047432,-50.563069206028985,0.06018140360019217,1.5679883655503224,0.08663546956210712,0.45000000000000245 +jmc_28,jmc_23,-7.465720270628921,0.034218263033781,-7.3474238069531745,0.03471722090528804,-0.1182964636757463,0.04874602499112714,-0.7199999999999974 +jmc_30,ejm_46,6.030978368062453,0.047265345700896626,5.351149765090641,0.04720148738530709,0.6798286029718125,0.06679815353443964,-0.3700000000000014 +jmc_30,jmc_27,3.212894176989629,0.039753422423706136,3.353850326960703,0.04040114452325584,-0.14095614997107384,0.05667968836529209,-0.340000000000001 +jmc_30,jmc_28,15.880746277691607,0.05089935109635592,14.513375160133057,0.05095529448301094,1.3673711175585503,0.0720221214480695,-0.040000000000002214 diff --git a/summaries/dec_09_2025/jacs/tyk2/dg_comparison_plot.png b/summaries/dec_09_2025/jacs/tyk2/dg_comparison_plot.png new file mode 100644 index 0000000..c394f42 Binary files /dev/null and b/summaries/dec_09_2025/jacs/tyk2/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/jacs/tyk2/dg_plot.png b/summaries/dec_09_2025/jacs/tyk2/dg_plot.png new file mode 100644 index 0000000..40687d0 Binary files /dev/null and b/summaries/dec_09_2025/jacs/tyk2/dg_plot.png differ diff --git a/summaries/dec_09_2025/jacs/tyk2/dg_results.csv b/summaries/dec_09_2025/jacs/tyk2/dg_results.csv new file mode 100644 index 0000000..e02c2d6 --- /dev/null +++ b/summaries/dec_09_2025/jacs/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,-9.853889852363336,0.05363566710266924,-9.54 +ejm_48,O=C(Nc1ccnc(NC(=O)C2CCCC2)c1)c1c(Cl)cccc1Cl,-9.463677983600048,0.06182744502387933,-9.0 +ejm_49,O=C(Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1)c1ccccc1,-8.106079934801052,0.0635868803164885,-7.75 +ejm_50,O=C(CO)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.065210392293247,0.04759240183811049,-8.98 +ejm_42,CCC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.429123073425686,0.046163610511472074,-9.78 +ejm_54,CCNC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-8.711897851719797,0.04582107046777121,-10.53 +ejm_43,CC(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-8.677520331123953,0.06142461837031098,-8.26 +ejm_44,CC(C)(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-7.503089704937387,0.059538575783601985,-7.42 +ejm_45,O=C(CC1CC1)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.484783269008403,0.04653286200997947,-9.56 +ejm_46,O=C(Nc1ccnc(NC(=O)C2CC2)c1)c1c(Cl)cccc1Cl,-10.636919569071367,0.05676443792890593,-11.31 +jmc_27,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2Cl)c1)c1c(Cl)cccc1Cl,-11.21555752678033,0.05951954329676289,-11.28 +ejm_47,O=C(Nc1ccnc(NC(=O)C2CCC2)c1)c1c(Cl)cccc1Cl,-9.78126392744629,0.057900289865335304,-9.7 +jmc_23,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2F)c1)c1c(Cl)cccc1Cl,-10.872010393975707,0.06168130577372775,-11.7 +ejm_55,COC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.317324142714872,0.05768448890773832,-9.21 +jmc_28,C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.47045967647966,0.05540422282884982,-10.98 +jmc_30,N#C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-11.351192370258847,0.05619428027935766,-10.94 diff --git a/summaries/dec_09_2025/malt1/README.md b/summaries/dec_09_2025/malt1/README.md new file mode 100644 index 0000000..8bffed7 --- /dev/null +++ b/summaries/dec_09_2025/malt1/README.md @@ -0,0 +1,38 @@ +# Malt1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.27 +- RMSE: 2.00 +- R²: 0.37 +- Kendall 𝜏: 0.54 +- Spearman ρ: 0.69 + +## System Details +- Ligands: 16 +- Host Atoms: 6224 +- Map Details: + - Edges: 26 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 13 + - Mean Dummy Atoms: 6.8 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 3.12 Hours +- Total Nanoseconds Simulated: 2931.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/malt1/ddg_results.csv b/summaries/dec_09_2025/malt1/ddg_results.csv new file mode 100644 index 0000000..0f58675 --- /dev/null +++ b/summaries/dec_09_2025/malt1/ddg_results.csv @@ -0,0 +1,27 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +1832576-04-1,1832577-09-9,1.5370991331877013,0.06336106000727346,-0.09746560316042988,0.06312084590934305,1.634564736348131,0.08943637466689008,1.645852349536163 +1832576-04-1,Pfizer-01-01,3.0165192147784006,0.070472272886879,1.5795478801827456,0.07089241100931883,1.436971334595655,0.099960368069335,1.1857247500970411 +1832576-04-1,Pfizer-01-02,-0.4489819597812316,0.06442669068848354,-2.2550755856093243,0.06414048817325181,1.8060936258280929,0.09091094926450052,1.4466222234101842 +2714550-01-1,1832577-09-9,0.8009385597153721,0.06148506890998349,-0.6881857383621649,0.06195716483637822,1.489124298077537,0.08728747890406481,0.38622292552512305 +Pfizer-01-01,1832577-09-9,-1.4475466939487742,0.07341453448687986,-1.5372717524408046,0.07354855525668151,0.08972505849203034,0.10391864055245528,0.46012759943912185 +Pfizer-01-02,Pfizer-01-08,-12.824181282679623,0.06339526870246659,-12.68914011013471,0.06097587015667253,-0.13504117254491205,0.08796031397864225,2.1342033016841935 +Pfizer-01-03,Pfizer-01-05,-13.012549389469907,0.05610460162267929,-16.552109786919328,0.055754032011923256,3.5395603974494216,0.07909638682535448,1.652050803490815 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+Pfizer-01-05,Pfizer-01-08,-0.962152983754582,0.05222223834238225,1.8224404443684739,0.05409270758871015,-2.7845934281230558,0.07518765318698462,0.22112446381280448 +Pfizer-01-05,Pfizer-01-13,3.4040871345895227,0.049190383064546706,3.6511013498527265,0.04814874430854719,-0.2470142152632036,0.06883309788558624,0.22112446381280448 +Pfizer-01-06,Pfizer-01-03,-3.4743621532255284,0.04962806446302177,-2.698074630754464,0.049918815820538406,-0.7762875224710645,0.07039057433542278,-1.6856811149845812 +Pfizer-01-06,Pfizer-01-04,-39.67322303738132,0.06885983957625705,-39.781893703690606,0.07012873243186787,0.10867066630929115,0.09828385736716062,-0.5493885220934902 +Pfizer-01-06,Pfizer-01-11,-35.8916139562956,0.0704054110359037,-43.15501069729774,0.07016712104338789,7.263396741002139,0.09939993349420309,0.18749415231903838 +Pfizer-01-07,2714550-01-1,-38.95903281703269,0.07092804399543783,-38.072055488746685,0.07074190623036458,-0.8869773282860064,0.10017586896116479,-2.3080896267484032 +Pfizer-01-07,Pfizer-01-01,-37.4106158479064,0.06958346093777501,-38.23138526706636,0.07155430067367288,0.8207694191599588,0.09980919787763673,-2.381994300662402 +Pfizer-01-07,Pfizer-01-12,-31.057036019329672,0.07216400268447946,-34.81462331864797,0.0718311519444613,3.7575872993182946,0.10182022231911422,0.013106474334934547 +Pfizer-01-09,2714550-01-1,-7.621642090132765,0.045983734205760726,-3.222789759141763,0.04773468431508299,-4.3988523309910015,0.06628049410020025,-2.3211961010833377 +Pfizer-01-09,Pfizer-01-02,-8.248757104643033,0.04015343185749602,-5.7736872437157105,0.045024318473054506,-2.4750698609273227,0.06032816377031223,-2.1342033016841935 +Pfizer-01-09,Pfizer-01-10,-18.071532292908547,0.03827262986285578,-16.611959270479982,0.04273172689790501,-1.4595730224285652,0.05736544848858326,0.0 +Pfizer-01-10,Pfizer-01-02,9.59216456856654,0.036303122488032344,10.5239621777884,0.040705459844509254,-0.931797609221859,0.05454219617446692,-2.1342033016841935 +Pfizer-01-13,Pfizer-01-12,13.739212325374723,0.05484979878873058,15.148812887969244,0.058223336604140655,-1.4096005625945212,0.07999035787195413,0.0 diff --git a/summaries/dec_09_2025/malt1/dg_comparison_plot.png b/summaries/dec_09_2025/malt1/dg_comparison_plot.png new file mode 100644 index 0000000..d7e8498 Binary files /dev/null and b/summaries/dec_09_2025/malt1/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/malt1/dg_plot.png b/summaries/dec_09_2025/malt1/dg_plot.png new file mode 100644 index 0000000..b0079a4 Binary files /dev/null and b/summaries/dec_09_2025/malt1/dg_plot.png differ diff --git a/summaries/dec_09_2025/malt1/dg_results.csv b/summaries/dec_09_2025/malt1/dg_results.csv new file mode 100644 index 0000000..2de4be4 --- /dev/null +++ b/summaries/dec_09_2025/malt1/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1832576-04-1,CO[C@@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.48014823461883,0.07071103914547633,-10.031196069300446 +1832577-09-9,CO[C@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-8.958752536048,0.06825412108519685,-8.385343719764283 +Pfizer-01-01,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2ccnn12,-9.041514026650265,0.07418719058526001,-8.845471319203405 +Pfizer-01-02,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-8.558498501192481,0.042366598499069485,-8.584573845890262 +2714550-01-1,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.56058598377385,0.05740605668925404,-8.771566645289406 +Pfizer-01-08,CCOc1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(C)nn12,-8.375795986778249,0.05568228467832463,-6.450370544206068 +Pfizer-01-03,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)n2n1,-8.322619468151073,0.06089234655504159,-8.323545811509687 +Pfizer-01-05,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)cn2n1,-5.1032810201598116,0.059986736157142055,-6.671495008018873 +Pfizer-01-11,Cc1cc2nnc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,-0.25410832750612256,0.05274975411131484,-6.450370544206068 +Pfizer-01-04,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,-6.526319928648176,0.039630416612098804,-7.187253218618596 +Pfizer-01-10,Cc1nc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-7.654774884195354,0.048997256907481454,-6.450370544206068 +Pfizer-01-12,Cc1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)ccc2cncn12,-6.274774736753354,0.04977967554534934,-6.450370544206068 +Pfizer-01-13,O=C(Nc1ccnc(C(F)(F)F)c1)Nc1cnc2ccnn2c1,-5.1838743533782585,0.054007555761801086,-6.450370544206068 +Pfizer-01-06,Cc1nc2c(C3CC3)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1C,-7.307098211891129,0.06558432705324162,-6.6378646965251065 +Pfizer-01-07,Cn1ncc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)c21,-9.854201889189344,0.06319814718158581,-6.463477018541003 +Pfizer-01-09,Cc1cn2c(C(C)C)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1,-6.147662528963184,0.049280540880454825,-6.450370544206068 diff --git a/summaries/dec_09_2025/merck/cdk8/README.md b/summaries/dec_09_2025/merck/cdk8/README.md new file mode 100644 index 0000000..c5e9c13 --- /dev/null +++ b/summaries/dec_09_2025/merck/cdk8/README.md @@ -0,0 +1,38 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.36 +- RMSE: 1.68 +- R²: 0.59 +- Kendall 𝜏: 0.65 +- Spearman ρ: 0.85 + +## System Details +- Ligands: 33 +- Host Atoms: 6224 +- Map Details: + - Edges: 58 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 16 + - Mean Dummy Atoms: 7.7 + - Median Dummy Atoms: 8.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 9.44 Hours +- Total Nanoseconds Simulated: 8668.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/cdk8/ddg_results.csv b/summaries/dec_09_2025/merck/cdk8/ddg_results.csv new file mode 100644 index 0000000..90c2cee --- /dev/null +++ b/summaries/dec_09_2025/merck/cdk8/ddg_results.csv @@ -0,0 +1,59 @@ +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) +16,13,26.381244175644365,0.07539186038258291,29.28896762828213,0.07514316933105088,-2.9077234526377636,0.10644448557375746,-1.9935981948721846 +16,14,-4.040869565187752,0.07328480900454687,-7.842336989893792,0.07258778403070754,3.80146742470604,0.1031486772640423,0.9524348831554853 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a/summaries/dec_09_2025/merck/cdk8/dg_plot.png b/summaries/dec_09_2025/merck/cdk8/dg_plot.png new file mode 100644 index 0000000..85a56ea Binary files /dev/null and b/summaries/dec_09_2025/merck/cdk8/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/cdk8/dg_results.csv b/summaries/dec_09_2025/merck/cdk8/dg_results.csv new file mode 100644 index 0000000..e096205 --- /dev/null +++ b/summaries/dec_09_2025/merck/cdk8/dg_results.csv @@ -0,0 +1,34 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +16,CNC(=O)c1ccc2[nH]nc(Cc3cccc(C)c3)c2c1,-7.728720929070393,0.07588864055572966,-9.292698790319301 +13,Cc1cccc(Cc2n[nH]c3cc(O)c(C(=O)N4CC[C@H](O)C4)cc23)c1,-10.573689213315832,0.08546752752039147,-11.286296985191486 +14,CNC(=O)c1ccc2[nH]nc(CC(C)C)c2c1,-3.9945065372013837,0.07850406682324816,-8.340263907163816 +15,CNC(=O)c1ccc2[nH]nc(Cc3ccc(OC)c(OC)c3)c2c1,-7.141793116860662,0.07307994418645138,-7.690060315684702 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+35,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CC(O)C5)cc34)cc2)cn1,-13.772247011877747,0.07985574418994308,-11.52802099480568 +40,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCNCC5)cc34)cc2)cn1,-13.335920856648082,0.07320544177424919,-11.1943977818631 +41,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCCCC5)cc34)cc2)cn1,-12.624391777830965,0.07227648637726226,-11.286296985191486 +43,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CCC(F)(F)C5)cc34)ccc21,-11.925659815348013,0.08191647900539432,-11.941250918631892 +44,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CC(O)C5)cc34)ccc21,-12.518613221240543,0.0797922673517732,-11.52802099480568 diff --git a/summaries/dec_09_2025/merck/cmet_neutral/README.md b/summaries/dec_09_2025/merck/cmet_neutral/README.md new file mode 100644 index 0000000..c07d254 --- /dev/null +++ b/summaries/dec_09_2025/merck/cmet_neutral/README.md @@ -0,0 +1,38 @@ +# Cmet Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.90 +- RMSE: 1.13 +- R²: 0.79 +- Kendall 𝜏: 0.63 +- Spearman ρ: 0.76 + +## System Details +- Ligands: 12 +- Host Atoms: 4580 +- Map Details: + - Edges: 19 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 26 + - Mean Dummy Atoms: 7.9 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 2.83 Hours +- Total Nanoseconds Simulated: 2485.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/cmet_neutral/ddg_results.csv b/summaries/dec_09_2025/merck/cmet_neutral/ddg_results.csv new file mode 100644 index 0000000..f157e99 --- /dev/null +++ b/summaries/dec_09_2025/merck/cmet_neutral/ddg_results.csv @@ -0,0 +1,20 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +CHEMBL3402744_300,CHEMBL3402745_200,3.478526633542116,0.04898121145804535,4.356651412686452,0.049037246889377474,-0.8781247791443357,0.06930952790480913,-0.24172400961419577 +CHEMBL3402744_300,CHEMBL3402747_3400,11.046486505698429,0.056943086266853536,11.665669460013033,0.059056771042986456,-0.6191829543146044,0.08203790148229077,1.447337948918152 +CHEMBL3402744_300,CHEMBL3402752_30000,18.70038667312315,0.05982097975740651,17.73247253735513,0.06248537051981253,0.9679141357680193,0.08650416838588933,2.74544018721291 +CHEMBL3402745_200,CHEMBL3402751_2100,19.574522461893263,0.07327804435865429,17.555129221463265,0.07510091348516466,2.0193932404299995,0.10492768458007207,1.4018070702091983 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b/summaries/dec_09_2025/merck/cmet_neutral/dg_comparison_plot.png new file mode 100644 index 0000000..45a77a6 Binary files /dev/null and b/summaries/dec_09_2025/merck/cmet_neutral/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/cmet_neutral/dg_plot.png b/summaries/dec_09_2025/merck/cmet_neutral/dg_plot.png new file mode 100644 index 0000000..0c9bb71 Binary files /dev/null and b/summaries/dec_09_2025/merck/cmet_neutral/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/cmet_neutral/dg_results.csv b/summaries/dec_09_2025/merck/cmet_neutral/dg_results.csv new file mode 100644 index 0000000..f33136b --- /dev/null +++ b/summaries/dec_09_2025/merck/cmet_neutral/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3402744_300,COC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-7.125183964496491,0.04752643171830985,-8.954086721804785 +CHEMBL3402745_200,CCOC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-8.083791077135645,0.04672964801053791,-9.19581073141898 +CHEMBL3402747_3400,Cc1noc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)n1,-7.6783920470762475,0.05759771856280276,-7.506748772886633 +CHEMBL3402752_30000,Cc1nc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)cs1,-6.105255191503699,0.057524371163047684,-6.208646534591875 +CHEMBL3402751_2100,Cc1csc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)n1,-6.261472587320181,0.0555955313062076,-7.794003661209782 +CHEMBL3402754_40,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-10.546596939074735,0.04034094929722,-10.155300901199226 +CHEMBL3402749_500,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)o1,-8.728096045854315,0.05969705059126396,-8.649550485464946 +CHEMBL3402755_4200,Cc1ccc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nn1,-8.53714041356029,0.05340636282485155,-7.3807737373835725 +CHEMBL3402748_5300,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)[nH]1,-6.418070463602734,0.06796063862083183,-7.242092522123443 +CHEMBL3402761_1,N#Cc1cccc(-c2ccc(=O)n(Cc3cccc(-c4ncc(OCCN5CCOCC5)cn4)c3)n2)c1,-14.532208619427033,0.06937630953232159,-12.354480842458102 +CHEMBL3402750_400,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)s1,-10.007510642452186,0.04998604286924475,-8.782580807592769 +CHEMBL3402753_200,Cc1ccc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-9.396168458049534,0.04680648985258485,-9.19581073141898 diff --git a/summaries/dec_09_2025/merck/cmet_positive/README.md b/summaries/dec_09_2025/merck/cmet_positive/README.md new file mode 100644 index 0000000..6b430f2 --- /dev/null +++ b/summaries/dec_09_2025/merck/cmet_positive/README.md @@ -0,0 +1,38 @@ +# Cmet Positive Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.14 +- RMSE: 1.33 +- R²: 0.67 +- Kendall 𝜏: 0.58 +- Spearman ρ: 0.79 + +## System Details +- Ligands: 12 +- Host Atoms: 4580 +- Map Details: + - Edges: 20 + - Min Dummy Atoms: 10 + - Max Dummy Atoms: 43 + - Mean Dummy Atoms: 24.6 + - Median Dummy Atoms: 23.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 4.22 Hours +- Total Nanoseconds Simulated: 3889.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/cmet_positive/ddg_results.csv b/summaries/dec_09_2025/merck/cmet_positive/ddg_results.csv new file mode 100644 index 0000000..f895773 --- /dev/null +++ b/summaries/dec_09_2025/merck/cmet_positive/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,CHEMBL3402760_1,-8.342977323178856,0.10278397902764419,-4.578096515263386,0.10460409321113522,-3.76488080791547,0.14665115976793044,-3.571900034865333 +CHEMBL3402741_400,CHEMBL3402763_90,-6.731381004604922,0.07521555392480513,-7.525311879918127,0.07598951108218634,0.7939308753132058,0.10691952743407065,-0.8892720743780677 +CHEMBL3402741_400,CHEMBL3402764_90,-11.180693869105266,0.07853842153602222,-13.043162373090158,0.07824054094182314,1.8624685039848927,0.11085966761739377,-0.8892720743780677 +CHEMBL3402743_42,CHEMBL3402742_23,-1.4664152848709424,0.07891818356610483,-0.6056262743998725,0.0811750214302258,-0.8607890104710698,0.11321423851075904,-0.3589957553370291 +CHEMBL3402743_42,CHEMBL3402758_10,-1.6754117954438497,0.08760461058318783,0.923563067692914,0.0884115201447683,-2.5989748631367635,0.12446350746198966,-0.8555468242551639 +CHEMBL3402743_42,CHEMBL3402762_1,3.551287742159515,0.09057321648168588,9.786219193228618,0.09245576452426475,-6.234931451069103,0.12942787929037788,-2.228266917861616 +CHEMBL3402743_42,CHEMBL3402765_11-charged-pKa-8.1,4.6957134104003915,0.07839351951137018,4.21196623853342,0.08238039023318282,0.48374717186697086,0.11371927099815167,-0.7987262536101402 +CHEMBL3402756_2.7,CHEMBL3402760_1,-0.22498036241282607,0.06964350795928369,0.6548118207662621,0.0687274199169109,-0.8797921831790882,0.09784516569207807,-0.5921417067147577 +CHEMBL3402757_6.5,CHEMBL3402742_23,-11.000705370785536,0.09102350455186833,-13.289726398016795,0.09240557157733939,2.2890210272312586,0.12970762521701948,0.75336866349987 +CHEMBL3402757_6.5,CHEMBL3402756_2.7,-3.035296860267289,0.07276372720655644,-2.5956351436318883,0.07191283971331576,-0.4396617166354008,0.1023035508309619,-0.5237607923099594 +CHEMBL3402758_10,CHEMBL3402757_6.5,11.423120542648723,0.07249517240637376,10.585874765930534,0.07229463626406736,0.8372457767181896,0.10238195375545273,-0.25681759458173514 +CHEMBL3402758_10,CHEMBL3402762_1,9.094607612830371,0.08605475363022046,11.182026710921589,0.0840082900007378,-2.0874190980912166,0.12026143775627335,-1.3727200936064523 +CHEMBL3402759_5.7,CHEMBL3402756_2.7,-6.853477165610582,0.06676528428813629,-5.558749247239674,0.06738971488542164,-1.2947279183709088,0.09486293722215267,-0.4454628959187488 +CHEMBL3402759_5.7,CHEMBL3402757_6.5,-3.4684291432896432,0.07262984772365995,-2.839939861319399,0.06902048840386671,-0.6284892819702439,0.10019442399590074,0.07829789639121063 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+CHEMBL3402765_11-charged-pKa-8.1,CHEMBL3402764_90,-0.8002975616551659,0.0819041027316546,-1.7048025712077761,0.08089201943234098,0.9045050095526103,0.11511646646818022,1.253087296235789 diff --git a/summaries/dec_09_2025/merck/cmet_positive/dg_comparison_plot.png b/summaries/dec_09_2025/merck/cmet_positive/dg_comparison_plot.png new file mode 100644 index 0000000..c4c1b53 Binary files /dev/null and b/summaries/dec_09_2025/merck/cmet_positive/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/cmet_positive/dg_plot.png b/summaries/dec_09_2025/merck/cmet_positive/dg_plot.png new file mode 100644 index 0000000..3a3c35a Binary files /dev/null and b/summaries/dec_09_2025/merck/cmet_positive/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/cmet_positive/dg_results.csv b/summaries/dec_09_2025/merck/cmet_positive/dg_results.csv new file mode 100644 index 0000000..b2ab29e --- /dev/null +++ b/summaries/dec_09_2025/merck/cmet_positive/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,-9.74455232601897,0.07552407990599802,-8.782580807592769 +CHEMBL3402760_1,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(C#N)c4)ccc3=O)c2)nc1,-13.348697538533877,0.05985683569955343,-12.354480842458102 +CHEMBL3402763_90,CC[NH+](CC)CCCOC(=O)Nc1cccc(CN2N=C(c3ccc(Cl)cc3)CSC2=O)c1,-9.162179647678826,0.08131668584389135,-9.671852881970837 +CHEMBL3402764_90,C[NH+](C)CCCOC(=O)Nc1cccc(Cn2nc(-c3ccc(F)cc3)ccc2=O)c1,-7.746497780052818,0.07618127317725329,-9.671852881970837 +CHEMBL3402743_42,C[NH+](C)CCCOC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-9.060245806523689,0.059546594861303,-10.126213924596485 +CHEMBL3402742_23,C[NH+](C)CCCOC(=O)Nc1cccc(CN2N=C(c3cc(F)cc(F)c3)CSC2=O)c1,-9.642916961987094,0.06839485911935614,-10.485209679933515 +CHEMBL3402758_10,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccnc4)ccc3=O)c2)nc1,-12.352744141151108,0.06356541451815102,-10.981760748851649 +CHEMBL3402762_1,C[N@H+]1CC[C@H](COc2cnc(-c3cccc(Cn4nc(-c5cccc(C#N)c5)ccc4=O)c3)nc2)CC1,-14.771455670757796,0.06917096049450396,-12.354480842458102 +CHEMBL3402765_11-charged-pKa-8.1,O=C(Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1)OCCC[NH+]1CCOCC1,-8.682456313853717,0.07174770538873076,-10.924940178206626 +CHEMBL3402756_2.7,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-12.344420923710992,0.07072812687408468,-11.762339135743344 +CHEMBL3402757_6.5,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(F)c4)ccc3=O)c2)nc1,-11.74466218075892,0.06019172228654328,-11.238578343433385 +CHEMBL3402759_5.7,COc1cccc(-c2ccc(=O)n(Cc3cccc(-c4ncc(OCCC[NH+](C)C)cn4)c3)n2)c1,-11.070337216012426,0.061063783954769774,-11.316876239824595 diff --git a/summaries/dec_09_2025/merck/eg5_neutral/README.md b/summaries/dec_09_2025/merck/eg5_neutral/README.md new file mode 100644 index 0000000..b44024d --- /dev/null +++ b/summaries/dec_09_2025/merck/eg5_neutral/README.md @@ -0,0 +1,38 @@ +# Eg5 Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.95 +- RMSE: 1.13 +- R²: 0.56 +- Kendall 𝜏: 0.42 +- Spearman ρ: 0.54 + +## System Details +- Ligands: 9 +- Host Atoms: 5906 +- Map Details: + - Edges: 15 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 22 + - Mean Dummy Atoms: 9.5 + - Median Dummy Atoms: 9.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 2.26 Hours +- Total Nanoseconds Simulated: 1916.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/eg5_neutral/ddg_results.csv b/summaries/dec_09_2025/merck/eg5_neutral/ddg_results.csv new file mode 100644 index 0000000..190cdbc --- /dev/null +++ b/summaries/dec_09_2025/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) +CHEMBL1078691,CHEMBL1084115,3.498870940839535,0.060886101526380576,1.8739203121531443,0.060686492208574715,1.6249506286863906,0.08596492130899744,0.7518419923407236 +CHEMBL1078691,CHEMBL1088740,4.811540192973895,0.06762144308307179,0.6405044007091493,0.06874505453951398,4.171035792264745,0.09642894839350821,1.4986951291095145 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+CHEMBL1085895,CHEMBL1088740,23.78423359250178,0.07586591210542039,19.856833671111495,0.07642507237966803,3.9273999213902857,0.10768671370148163,2.1714463472165977 +CHEMBL1085895,CHEMBL1093088,19.888059040771406,0.07964942587137283,18.55424249901087,0.07791257974038289,1.3338165417605359,0.11141993144604262,-0.36135680698486067 +CHEMBL1089056,CHEMBL1078998,-3.6653142010200805,0.057126477882899415,-3.139893497116101,0.05870032135033663,-0.5254207039039794,0.0819094756541524,-0.9351535351387962 +CHEMBL1089393,CHEMBL1085895,-21.27201361175744,0.0742976612058365,-18.1549225865761,0.07189820236352483,-3.1170910251813417,0.10339000901326796,-2.4927770677144205 +CHEMBL1089393,CHEMBL1089056,7.143250184911247,0.0467962912356174,10.016301924917935,0.044658966652875186,-2.8730517400066873,0.06468629047882819,-1.0681838572666138 +CHEMBL1089393,CHEMBL1093088,-4.608391517258999,0.06462207678282392,-2.132830148458536,0.06188754379651064,-2.475561368800464,0.08947670582274592,-2.854133874699281 +CHEMBL1093088,CHEMBL1088740,6.577441656306805,0.06602395454541765,3.7854671124189156,0.06527871766336313,2.7919745438878887,0.09284650533858803,2.532803154201458 diff --git a/summaries/dec_09_2025/merck/eg5_neutral/dg_comparison_plot.png b/summaries/dec_09_2025/merck/eg5_neutral/dg_comparison_plot.png new file mode 100644 index 0000000..e030b75 Binary files /dev/null and b/summaries/dec_09_2025/merck/eg5_neutral/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/eg5_neutral/dg_plot.png b/summaries/dec_09_2025/merck/eg5_neutral/dg_plot.png new file mode 100644 index 0000000..f167b09 Binary files /dev/null and b/summaries/dec_09_2025/merck/eg5_neutral/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/eg5_neutral/dg_results.csv b/summaries/dec_09_2025/merck/eg5_neutral/dg_results.csv new file mode 100644 index 0000000..78593a0 --- /dev/null +++ b/summaries/dec_09_2025/merck/eg5_neutral/dg_results.csv @@ -0,0 +1,10 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1078691,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)cc1)N2,-11.862568490293613,0.04584526062127323,-10.252188960099543 +CHEMBL1084115,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccsc1)N2,-10.255039614184465,0.046838243266844895,-9.50034696775882 +CHEMBL1088740,Cc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-7.174013187065549,0.042360580995400084,-8.753493830990028 +CHEMBL1089056,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-10.007973636470588,0.03244310258334149,-9.50034696775882 +CHEMBL1078774,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)c(F)c1)N2,-12.065950980169639,0.040629848652422945,-10.665418883925756 +CHEMBL1078998,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1cccs1)N2,-10.427222319115792,0.048785738875708966,-10.435500502897614 +CHEMBL1085895,O=C(NCCCO)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-10.864039734130206,0.05720808700226173,-10.924940178206626 +CHEMBL1093088,FC(F)(F)c1ccc2c(c1)[C@H]1O[C@@H](Cn3cncn3)CC[C@H]1[C@H](c1ccccc1)N2,-9.785904412121704,0.05740443555812216,-11.286296985191486 +CHEMBL1089393,Clc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-7.3079840137693255,0.04438838971996431,-8.432163110492205 diff --git a/summaries/dec_09_2025/merck/eg5_positive/README.md b/summaries/dec_09_2025/merck/eg5_positive/README.md new file mode 100644 index 0000000..54cb835 --- /dev/null +++ b/summaries/dec_09_2025/merck/eg5_positive/README.md @@ -0,0 +1,38 @@ +# Eg5 Positive Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.78 +- RMSE: 1.07 +- R²: 0.00 +- Kendall 𝜏: 0.07 +- Spearman ρ: 0.11 + +## System Details +- Ligands: 19 +- Host Atoms: 5906 +- Map Details: + - Edges: 33 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 25 + - Mean Dummy Atoms: 12.3 + - Median Dummy Atoms: 12.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 5.42 Hours +- Total Nanoseconds Simulated: 5482.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/eg5_positive/ddg_results.csv b/summaries/dec_09_2025/merck/eg5_positive/ddg_results.csv new file mode 100644 index 0000000..5fc5ce7 --- /dev/null +++ b/summaries/dec_09_2025/merck/eg5_positive/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) +CHEMBL1077204,CHEMBL1084676,8.490862665118488,0.06117300192782964,8.113461309557255,0.060679760570934174,0.37740135556123366,0.08616362055884227,0.33362321294258274 +CHEMBL1077204,CHEMBL1085692,22.946572488998555,0.075669695748252,22.575407600691037,0.07607549974550444,0.37116488830751876,0.10730044042855216,-0.2801996016983872 +CHEMBL1077227,CHEMBL1084935,14.190074342337532,0.07867370523199776,12.934207368670156,0.07914977288573538,1.2558669736673753,0.1115985593222187,0.7958805930193142 +CHEMBL1077227,CHEMBL1086410,3.3071238808373264,0.059228638843748634,3.092494329258001,0.05908585111483666,0.21462955157932487,0.08366103908778479,-0.133030322127821 +CHEMBL1082248,CHEMBL1085666,-14.55946954758622,0.06853121832318909,-15.853786453117547,0.0659491366793528,1.294316905531327,0.09510949749427008,1.1309960839922635 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a/summaries/dec_09_2025/merck/eg5_positive/dg_plot.png b/summaries/dec_09_2025/merck/eg5_positive/dg_plot.png new file mode 100644 index 0000000..c2714f0 Binary files /dev/null and b/summaries/dec_09_2025/merck/eg5_positive/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/eg5_positive/dg_results.csv b/summaries/dec_09_2025/merck/eg5_positive/dg_results.csv new file mode 100644 index 0000000..de865aa --- /dev/null +++ b/summaries/dec_09_2025/merck/eg5_positive/dg_results.csv @@ -0,0 +1,20 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1077204,C[NH+](C)CCNC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.059382430194216,0.06479057069134446,-11.11479107097947 +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,-10.348729447192916,0.08056328217387079,-10.781167858036888 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System Details +- Ligands: 42 +- Host Atoms: 1770 +- Map Details: + - Edges: 75 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 2.0 + - Median Dummy Atoms: 1.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 7.74 Hours +- Total Nanoseconds Simulated: 8324.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/hif2a/ddg_results.csv b/summaries/dec_09_2025/merck/hif2a/ddg_results.csv new file mode 100644 index 0000000..72416b2 --- /dev/null +++ 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Atoms: 13 + - Mean Dummy Atoms: 3.8 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 6.58 Hours +- Total Nanoseconds Simulated: 7397.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/hif2a_jmc2023_jmc/ddg_results.csv b/summaries/dec_09_2025/merck/hif2a_jmc2023_jmc/ddg_results.csv new file mode 100644 index 0000000..901014b --- /dev/null +++ b/summaries/dec_09_2025/merck/hif2a_jmc2023_jmc/ddg_results.csv @@ -0,0 +1,69 @@ +mol_a,mol_b,complex_pred_dg 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@@ -0,0 +1,38 @@ +# Pfkfb3 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.92 +- RMSE: 1.12 +- R²: 0.33 +- Kendall 𝜏: 0.39 +- Spearman ρ: 0.56 + +## System Details +- Ligands: 40 +- Host Atoms: 7834 +- Map Details: + - Edges: 69 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 16 + - Mean Dummy Atoms: 3.7 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 8.76 Hours +- Total Nanoseconds Simulated: 7678.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/pfkfb3/ddg_results.csv b/summaries/dec_09_2025/merck/pfkfb3/ddg_results.csv new file mode 100644 index 0000000..5d40fec --- /dev/null +++ b/summaries/dec_09_2025/merck/pfkfb3/ddg_results.csv @@ -0,0 +1,70 @@ +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) +19,23,-3.1646361023706557,0.038757872693830096,-3.0144284287061365,0.04037248533511013,-0.15020767366451945,0.05596525947304115,-0.36593561542120234 +19,33,-5.689591639851935,0.053352518710425005,-2.8537944217124736,0.05375875537917401,-2.8357972181394615,0.0757396529742784,-1.0626948334705881 +20,42,-2.437501018541109,0.05246862402920869,-2.5588700252783725,0.05183796394685973,0.12136900673726363,0.07375724380475714,0.04995926363476655 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b/summaries/dec_09_2025/merck/pfkfb3/dg_results.csv new file mode 100644 index 0000000..2e4cf73 --- /dev/null +++ b/summaries/dec_09_2025/merck/pfkfb3/dg_results.csv @@ -0,0 +1,41 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +19,Cn1ccc2ccc(-c3cc(Nc4ccccc4)cc4nccnc34)cc21,-7.3701098117807335,0.08118531579255094,-7.597684371217873 +23,Cn1ccc2ccc(-c3cc(Nc4cccnc4)cc4nccnc34)cc21,-7.813353423984711,0.08158563347643431,-7.963619986639076 +33,Cn1ccc2ccc(-c3cc(Nc4cnccc4C#N)cc4nccnc34)cc21,-10.060470734472553,0.06856137649416394,-8.66037920468846 +20,COc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-9.190192950568314,0.087761846332526,-8.569347907703273 +42,CSc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-8.991302390293429,0.08840860243545064,-8.519388644068506 +44,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(Br)cc2)c2nccnc2c1,-8.65916905691659,0.06679909172769731,-10.01046495048535 +24,Cn1ccc2ccc(-c3cc(Nc4ccccc4C#N)cc4nccnc34)cc21,-9.034231813176103,0.07508901953558726,-8.924999745202046 +26,Cn1ccc2ccc(-c3cc(Nc4ccccc4C(N)=O)cc4nccnc34)cc21,-8.712467477136489,0.07210890070392906,-9.226389986052087 +29,Cn1ccc2ccc(-c3cc(Nc4ccccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.400023026945211,0.06060174119921069,-9.70592871414551 +34,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(N)=O)cc4nccnc34)cc21,-10.350178338709334,0.07690024960323914,-10.034314721268096 +37,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(=O)NC4CCOCC4)cc4nccnc34)cc21,-10.487015419772233,0.0889503684303662,-10.05915851439343 +60,CC1(C)COc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.282277280264207,0.07018701197390645,-8.194315708437303 +35,Cn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.343747167066264,0.05591728823788903,-10.201778825003053 +57,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ccn(C(F)F)c3c2)c2nccnc2c1,-9.746354533516518,0.07379256886576957,-10.539443848422694 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+43,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(Br)c2)c2nccnc2c1,-9.24572331561799,0.06332099887272803,-8.047337448876245 +39,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(N)c2)c2nccnc2c1,-6.491923393382063,0.07597347382502467,-7.242205016653798 +46,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(C(F)(F)F)cc2)c2nccnc2c1,-6.970781121022772,0.06924582168819893,-7.908173068126793 +49,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(N)cc2)c2nccnc2c1,-6.171151186516641,0.07242401673724193,-7.983570733571719 +62,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nonc3c2)c2nccnc2c1,-9.605345191084398,0.06014203854134305,-7.739510346982183 +63,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nsnc3c2)c2nccnc2c1,-8.455459407936655,0.06907834430264533,-8.614812615729898 +48,COc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.968630342799685,0.07716471694259246,-8.056085438002924 +47,CCc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.331273889054531,0.07912035989595627,-8.385209272895247 +64,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ncsc3c2)c2nccnc2c1,-8.10277674561578,0.06911660003271318,-9.480798830844416 +52,CCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.783406731751223,0.07448864870224116,-10.459837137539063 +54,CC(C)n1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-7.63571825370998,0.08153428914339643,-8.230388525015318 +55,Cn1ccc2c(F)cc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-10.254486466002534,0.05893116195335077,-10.701561147153257 +56,Cc1cc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc2c1ccn2C,-10.271526039439753,0.06323184553575363,-10.631343051751081 +58,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)CCO3)c2nccnc2c1,-9.815561631024858,0.08158009204167889,-9.189878694795562 +59,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)OCCO3)c2nccnc2c1,-9.230281243466168,0.09000649294953302,-8.16557277738621 +65,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3scnc3c2)c2nccnc2c1,-9.316592282794462,0.04872930167887656,-9.546824891562647 +67,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)nc3c2)c2nccnc2c1,-11.472336547650094,0.059520276463895065,-10.307258678496837 +68,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)cc3c2)c2nccnc2c1,-10.298169121535278,0.059019233138294096,-9.838959036273334 diff --git a/summaries/dec_09_2025/merck/shp2/README.md b/summaries/dec_09_2025/merck/shp2/README.md new file mode 100644 index 0000000..9a5ba43 --- /dev/null +++ b/summaries/dec_09_2025/merck/shp2/README.md @@ -0,0 +1,38 @@ +# Shp2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.49 +- RMSE: 1.84 +- R²: 0.21 +- Kendall 𝜏: 0.29 +- Spearman ρ: 0.40 + +## System Details +- Ligands: 26 +- Host Atoms: 8422 +- Map Details: + - Edges: 48 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 25 + - Mean Dummy Atoms: 5.4 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 8.26 Hours +- Total Nanoseconds Simulated: 5928.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/shp2/ddg_results.csv b/summaries/dec_09_2025/merck/shp2/ddg_results.csv new file mode 100644 index 0000000..49636e3 --- /dev/null +++ b/summaries/dec_09_2025/merck/shp2/ddg_results.csv @@ -0,0 +1,49 @@ +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,Example 23,-10.806901383638763,0.06018556567506053,-10.630544748833383,0.0612043427048648,-0.17635663480537916,0.08583865027807441,-1.5959089907842374 +11,Example 23,-7.586771338614979,0.06665916519117572,-5.138552061811538,0.06650419503456345,-2.448219276803442,0.09416077878384241,-2.401074976228418 +3,6,-13.371662115319577,0.07681740966497252,-11.802571546949139,0.07485688589381534,-1.5690905683704395,0.10725888211871269,-2.583036201887811 +4,6,-11.072304026160372,0.08093287303112603,-10.7896164984634,0.08007657162441027,-0.28268752769697053,0.11385248025489685,-2.2216793949029503 +4,Example 14,44.688503405198155,0.10198541134745909,50.987208202226796,0.09431445938453825,-6.298704797028645,0.13891091165458586,-3.980730198782025 +4,Example 27,67.91483281280186,0.06926733601195759,66.55448664015628,0.06930658676369582,1.3603461726455748,0.09798656442098137,-2.7132072151203728 +7,6,-25.38303673397642,0.06968834595049063,-24.338635700179292,0.06786951563613706,-1.044401033797129,0.09727659900510048,-0.9594901697802434 +Example 14,3,-44.58200727996624,0.09413479615794276,-49.870659200912556,0.09050272951088166,5.2886519209463145,0.13058370456001486,4.342087005766886 +Example 14,Example 27,21.982937120859606,0.08812952701319927,15.615217332030387,0.0833470328238457,6.367719788829221,0.12129938751745381,1.2675229836616524 +Example 1,7,19.491678345748852,0.07352829652522132,18.307524046447455,0.07222738638984763,1.1841542993013991,0.10306893680740681,1.9235839513310684 +Example 1,Example 3,-7.7605452387124805,0.07409441962564638,-5.64810705438916,0.07055355860172416,-2.11243818432332,0.10231220675475775,0.7771021976732414 +Example 1,Example 4,-6.336647594645157,0.07235005914333399,-5.3700347478642065,0.07060273852352998,-0.9666128467809502,0.10109044339138033,0.7919761025218072 +Example 1,Example 5,3.1395478422115657,0.05043440005566086,2.032948195727868,0.0475003929787704,1.1065996464836978,0.06928142638624053,1.4339357903539591 +Example 22,10,11.064372461330619,0.0651316349200651,11.834706107168948,0.06548612135968454,-0.7703336458383283,0.09236104134371793,2.0975000377510162 +Example 22,11,6.385961721264019,0.07241284950258643,6.3463470058726745,0.0705347302485046,0.03961471539134401,0.1010879267979789,2.9026660231951964 +Example 22,Example 1,-67.37452352876896,0.053609825992091166,-67.75006381679063,0.05227209204394141,0.3755402880216632,0.07487579748859156,0.2522139828111576 +Example 22,Example 24,0.3906228067553098,0.04408294039466914,-0.7357051154555255,0.04627490229306292,1.1263279222108353,0.0639114404161921,0.16262102901980635 +Example 22,Example 25,2.1837138519540806,0.05483248666839103,0.6669347611927128,0.05516295737917854,1.516779090761368,0.07777887541650592,0.37121625155419696 +Example 22,Example 26,0.11083143403620077,0.053407777314927726,-0.7450690073754473,0.053068046346795364,0.855900441411648,0.0752901601856878,0.2815209870088881 +Example 22,Example 28,24.26779339101987,0.08551811570982325,24.77922528108788,0.08447772031871606,-0.5114318900680067,0.12020745960549174,0.7863357641631342 +Example 22,Example 29,9.102467799373755,0.08401736137425492,10.937014074875874,0.0850140359216563,-1.8345462755021178,0.11952532499843208,1.6260883163945343 +Example 22,Example 9,-11.786868510922409,0.07882124385720342,-6.4782915135202535,0.07775549941344449,-5.308576997402156,0.1107190415973282,0.4475017016926592 +Example 24,Example 25,-2.6487534762964517,0.05432016423179995,-3.2929484491996543,0.05457381920824875,0.6441949729032027,0.07699988302032892,0.2085952225343906 +Example 26,Example 24,3.625729651469,0.056700699984424695,3.1607207464907923,0.057946813243071944,0.4650089049782076,0.08107282247307786,-0.11889995798908173 +Example 26,Example 25,-1.0022562014223546,0.060467149363169305,-1.2699270988106568,0.060456789407204836,0.267670897388302,0.08550613742612248,0.08969526454530886 +Example 28,Example 23,-21.724281841523464,0.08287040827180965,-23.450656007681136,0.08184929310248319,1.7263741661576721,0.11647665580927631,-0.28474471719635547 +Example 29,Example 23,-9.857171328142211,0.0816205021353558,-9.582172380586124,0.08224631277639989,-0.27499894755608867,0.11587218101917743,-1.1244972694277557 +Example 2,Example 30,33.48090367893246,0.04621907893526477,36.615583647937996,0.04584350024678618,-3.1346799690055427,0.06509861574950207,-0.886345539506191 +Example 2,Example 4,-8.542810870322315,0.07365621336344987,-6.322055853712648,0.07323578190617945,-2.2207550166096666,0.10386875140508589,0.07559798666580186 +Example 2,Example 6,-9.18732979469151,0.04729402079690843,-7.503201275271475,0.04545551029607346,-1.684128519420035,0.06559670585795331,-0.7979687379277243 +Example 30,Example 3,-43.20752771689442,0.0747155191970233,-43.54639808959099,0.07329009190412734,0.33887037269657516,0.10466062478409055,0.9470696213234271 +Example 30,Example 5,-32.26147843499993,0.055723813725385624,-35.806303325321345,0.05394125074489869,3.5448248903214137,0.07755515423249128,1.6039032140041447 +Example 4,Example 3,-0.25130097059443524,0.03617991731183523,-0.2439573128107277,0.034623224731018164,-0.007343657783707574,0.05007748104154024,-0.014873904848565751 +Example 6,6,-0.07981622708923485,0.06031415778507434,0.5885243017649247,0.058170359967594,-0.6683405288541595,0.08379491874858705,1.0456844036225441 +Example 6,7,25.20906652871596,0.07743097126409731,24.57960546835509,0.07468034890883028,0.629461060360872,0.10757653007996722,2.0051745734027873 +Example 6,Example 5,9.925174835399552,0.05832137774713327,7.851465955202567,0.056500096104292255,2.073708880196986,0.08120125591465979,1.515526412425678 +Example 8,Example 23,7.958444467991869,0.06946261425882141,3.4041655903534203,0.0707684947844146,4.55427887763845,0.09916266754036793,0.9780252822166582 +Example 9,6,-60.40188343360922,0.06573684652026993,-66.5928055578631,0.06633852260509777,6.190922124253884,0.09339235820909864,0.7688060626693235 +Example 9,Example 8,4.480538363265982,0.051537505712358,3.892716175727107,0.051935066926336634,0.587822187538875,0.07316669783237725,-0.9239359369425386 +SHP099-1/Example 7,10,15.558543788694298,0.04568452194074488,14.222326665480844,0.04785788079964331,1.3362171232134539,0.06616231782205992,2.614505349709493 +SHP099-1/Example 7,11,11.536538714849339,0.05642845516672247,9.26352449530399,0.056010239915897465,2.2730142195453493,0.079506713728711,3.419671335153674 +SHP099-1/Example 7,Example 28,28.369920840816004,0.0807297163554194,27.468632172644796,0.07748295332223126,0.9012886681712076,0.1118968058452141,1.3033410761216113 +SHP099-1/Example 7,Example 29,13.98171311297539,0.0758084644163506,13.270258209299113,0.0762935536704575,0.7114549036762775,0.10755291538973769,2.1430936283530118 +SHP099-1/Example 7,Example 30,-27.421471669298953,0.0426199311757514,-26.637518163011283,0.04409779627932629,-0.7839535062876708,0.06132759713309131,0.599251871119449 +SHP099-1/Example 7,Example 8,-2.8820243600181374,0.06026897940181815,0.15627962445840338,0.059339280182831744,-3.0383039844765407,0.0845783663282366,0.0405710767085977 +SHP836-2,3,0.228605425868135,0.05479397170043765,1.2711811659212227,0.05437738907939382,-1.0425757400530877,0.07719637153260599,1.2580347500394595 +SHP836-2,6,-12.408086274106353,0.07010087594891685,-10.907361879362057,0.06730760428304045,-1.500724394744297,0.09718254165809717,-1.3250014518483515 +SHP836-2,Example 27,65.87513850922643,0.0467861313759828,66.66081028821446,0.04709990056030181,-0.7856717789880311,0.06638782058420838,-1.8165292720657737 diff --git a/summaries/dec_09_2025/merck/shp2/dg_comparison_plot.png b/summaries/dec_09_2025/merck/shp2/dg_comparison_plot.png new file mode 100644 index 0000000..a8996c3 Binary files /dev/null and b/summaries/dec_09_2025/merck/shp2/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/shp2/dg_plot.png b/summaries/dec_09_2025/merck/shp2/dg_plot.png new file mode 100644 index 0000000..dd4fa2a Binary files /dev/null and b/summaries/dec_09_2025/merck/shp2/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/shp2/dg_results.csv b/summaries/dec_09_2025/merck/shp2/dg_results.csv new file mode 100644 index 0000000..21920f0 --- /dev/null +++ b/summaries/dec_09_2025/merck/shp2/dg_results.csv @@ -0,0 +1,27 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)cn2)CC1,-8.22874134061293,0.05510257220978988,-7.198715959005226 +Example 23,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Cl)CC1,-8.520631758343953,0.05372423153699579,-8.794624949789464 +11,CNc1nc(N2CCC(C)([NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-6.93119981479151,0.06538504550653886,-6.393549973561046 +3,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-6.98827977953375,0.08561977132829593,-5.496872030506449 +6,Nc1nc(N2CCC([NH3+])CC2)ncc1-c1cccc(Cl)c1Cl,-7.949676788997001,0.057574388931384314,-8.07990823239426 +4,C[C@@H]1CN(c2ncc(-c3ccc(Cl)c(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-7.596201573343923,0.08614071998595325,-5.85822883749131 +Example 14,Nc1nc(N2CC[C@@H](C[NH3+])C2)cnc1-c1cccc(Cl)c1Cl,-13.017578030310494,0.09864003543079276,-9.838959036273334 +Example 27,C[C@@H]1CN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-6.619960714951542,0.08038139699281178,-8.571436052611682 +7,C[NH+](C)C1CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-6.786359592027952,0.06443552265147721,-7.120418062614016 +Example 1,CC1([NH3+])CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-7.422484514178207,0.04506773999311022,-9.044002013945084 +Example 3,CC1([NH3+])CCN(c2ncc(-c3ccc(Cl)s3)c(N)n2)CC1,-9.114025662163279,0.05887368658811615,-8.266899816271843 +Example 4,Cc1ccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)s1,-8.923285371695242,0.060129868230438956,-8.252025911423278 +Example 5,COc1cc(Cl)c(Cl)c(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1,-6.1504891080064,0.05402282849032914,-7.610066223591126 +Example 22,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Br)CC1,-7.634353744308338,0.043437445942803334,-9.296215996756242 +Example 24,Cc1nc(-c2cccc(Cl)c2Cl)c(N)nc1N1CCC(C)([NH3+])CC1,-6.525606056458711,0.06409535532472987,-9.133594967736435 +Example 25,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C#N)CC1,-6.135293482856085,0.07276275858662576,-8.924999745202046 +Example 26,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C(N)=O)CC1,-6.737452825534086,0.06302372589936564,-9.014695009747355 +Example 28,CC1([NH3+])CCN(c2cnc(-c3cccc4cc[nH]c34)c(N)n2)CC1,-8.969682252220954,0.07911576172537835,-8.509880232593108 +Example 29,CC1([NH3+])CCN(c2cnc(C3=CCCCC3)c(N)n2)CC1,-8.784489213444065,0.06692119353944079,-7.670127680361708 +Example 9,Nc1nc(N2CCC(C[NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-13.522205173182686,0.05239274559153513,-8.848714295063584 +Example 2,Cc1cccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1Cl,-6.477485860927828,0.04775617727059129,-8.32762389808908 +Example 30,CC1([NH3+])CCN(c2nnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.813529934500847,0.045298741614063914,-9.21396943759527 +Example 6,CC1([NH3+])CCN(c2ncc(-c3cc(O)cc(Cl)c3Cl)c(N)n2)CC1,-7.86740126182722,0.048214570571908234,-9.125592636016805 +Example 8,CC1(C[NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-12.807801320829764,0.06283679459753526,-9.772650232006121 +SHP099-1/Example 7,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.40603385840856,0.043956201087822805,-9.81322130871472 +SHP836-2,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-6.001650286451204,0.07600928702101391,-6.754906780545908 diff --git a/summaries/dec_09_2025/merck/syk_negative/README.md b/summaries/dec_09_2025/merck/syk_negative/README.md new file mode 100644 index 0000000..d79335e --- /dev/null +++ b/summaries/dec_09_2025/merck/syk_negative/README.md @@ -0,0 +1,38 @@ +# Syk Negative Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.48 +- RMSE: 0.66 +- R²: 0.77 +- Kendall 𝜏: 0.60 +- Spearman ρ: 0.71 + +## System Details +- Ligands: 6 +- Host Atoms: 4667 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 38 + - Mean Dummy Atoms: 15.6 + - Median Dummy Atoms: 7.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 1.92 Hours +- Total Nanoseconds Simulated: 1727.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/syk_negative/ddg_results.csv b/summaries/dec_09_2025/merck/syk_negative/ddg_results.csv new file mode 100644 index 0000000..6ac1313 --- /dev/null +++ b/summaries/dec_09_2025/merck/syk_negative/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) +CHEMBL3264994,CHEMBL3264995,-11.682449240895595,0.08374376240071922,-7.609482894044929,0.08175299371835403,-4.0729663468506665,0.11703234477246599,-2.5925659381562567 +CHEMBL3264994,CHEMBL3265001,0.082830780061347,0.08276626817989541,3.0203053796581907,0.08302530820359805,-2.9374745995968436,0.11723249101989094,-2.2468985830169808 +CHEMBL3264995,CHEMBL3265000,-11.357075622176913,0.06379885027274251,-11.214617610191903,0.06241405464813145,-0.14245801198501004,0.0892513726154604,0.5739938399963156 +CHEMBL3264995,CHEMBL3265001,19.35596552162029,0.060831994234526336,18.924934146502324,0.059646643050841656,0.431031375117971,0.08519538455681719,0.34566735513927593 +CHEMBL3264997,CHEMBL3264994,10.528344445066136,0.08499011188248,7.186897156204801,0.0838332568988278,3.3414472888613345,0.1193789515788329,1.1853758538405335 +CHEMBL3264997,CHEMBL3264998,-0.484659961346954,0.07040063257921741,-1.3666469003701258,0.07057471713671676,0.8819869390231719,0.09968470176753075,-0.7336044857199532 +CHEMBL3264997,CHEMBL3265001,10.505964195916647,0.0681468206711121,10.710556284878093,0.0683437128360818,-0.20459208896144626,0.09651348222814013,-1.061522729176447 +CHEMBL3264998,CHEMBL3265000,-13.070746042785611,0.07313676526388985,-12.748848237372616,0.07457189989061759,-0.3218978054129936,0.10445072851139726,-0.09959175859945434 +CHEMBL3264998,CHEMBL3265001,19.289339292817385,0.06826274740609209,19.53789264447993,0.06908514854993518,-0.24855335166254303,0.0971213696031648,-0.32791824345649395 +CHEMBL3265001,CHEMBL3265000,-30.796299500498787,0.07846948052930794,-30.748248891989235,0.07841399919689292,-0.04805060850955094,0.11093337930753648,0.22832648485703963 diff --git a/summaries/dec_09_2025/merck/syk_negative/dg_comparison_plot.png b/summaries/dec_09_2025/merck/syk_negative/dg_comparison_plot.png new file mode 100644 index 0000000..4c78968 Binary files /dev/null and b/summaries/dec_09_2025/merck/syk_negative/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/syk_negative/dg_plot.png b/summaries/dec_09_2025/merck/syk_negative/dg_plot.png new file mode 100644 index 0000000..947dfe6 Binary files /dev/null and b/summaries/dec_09_2025/merck/syk_negative/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/syk_negative/dg_results.csv b/summaries/dec_09_2025/merck/syk_negative/dg_results.csv new file mode 100644 index 0000000..7918d99 --- /dev/null +++ b/summaries/dec_09_2025/merck/syk_negative/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3264994,CC(C)(C)c1ccc(Nc2nc(-c3cccc(NC(=O)c4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1,-8.732140075529973,0.05505710192768262,-9.865858249826928 +CHEMBL3264995,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-12.393832672243748,0.04931168131575572,-12.458424187983185 +CHEMBL3265001,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5nnn[n-]5)cc4)c3)cn3ccnc23)cc1OC,-12.021286334419836,0.03912374291845045,-12.112756832843909 +CHEMBL3265000,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(=O)[N-]S(C)(=O)=O)cc4)c3)cn3ccnc23)cc1OC,-12.232911082378331,0.05258111314545598,-11.88443034798687 +CHEMBL3264997,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4cccc(C(=O)[O-])c4)c3)cn3ccnc23)cc1OC,-12.136851931218088,0.05484682500611174,-11.051234103667463 +CHEMBL3264998,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(CC(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-11.640520215905788,0.05277411136419721,-11.784838589387416 diff --git a/summaries/dec_09_2025/merck/syk_neutral/README.md b/summaries/dec_09_2025/merck/syk_neutral/README.md new file mode 100644 index 0000000..df8aeb2 --- /dev/null +++ b/summaries/dec_09_2025/merck/syk_neutral/README.md @@ -0,0 +1,38 @@ +# Syk Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.35 +- RMSE: 1.69 +- R²: 0.01 +- Kendall 𝜏: -0.05 +- Spearman ρ: -0.10 + +## System Details +- Ligands: 38 +- Host Atoms: 4667 +- Map Details: + - Edges: 67 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 7.69 Hours +- Total Nanoseconds Simulated: 8189.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/syk_neutral/ddg_results.csv b/summaries/dec_09_2025/merck/syk_neutral/ddg_results.csv new file mode 100644 index 0000000..1d46790 --- /dev/null +++ b/summaries/dec_09_2025/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,CHEMBL3265019,19.867083292196018,0.06669866513934404,21.184118265628545,0.0652927792549314,-1.3170349734325275,0.09333733954963333,-0.20261722132296622 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MUE: 0.59 +- RMSE: 0.75 +- R²: 0.60 +- Kendall 𝜏: 0.50 +- Spearman ρ: 0.66 + +## System Details +- Ligands: 21 +- Host Atoms: 4074 +- Map Details: + - Edges: 39 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 10 + - Mean Dummy Atoms: 3.5 + - Median Dummy Atoms: 3.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 3.86 Hours +- Total Nanoseconds Simulated: 3850.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/tnks2_neutral/ddg_results.csv b/summaries/dec_09_2025/merck/tnks2_neutral/ddg_results.csv new file mode 100644 index 0000000..26f4a2c --- /dev/null +++ b/summaries/dec_09_2025/merck/tnks2_neutral/ddg_results.csv @@ -0,0 +1,40 @@ +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,5c,-2.147599157800581,0.06767279638272765,1.121012597981137,0.07020343932766494,-3.268611755781718,0.09750964190115381,-1.418601554367181 +1a,5d,-7.156745871211772,0.06005074254423727,-3.64059914263573,0.06039337301449309,-3.516146728576042,0.08516719546974627,-2.349004747544686 +1b,1a,0.4303993668675642,0.047034374024482316,-1.6402582723013908,0.04649916565421132,2.0706576391689553,0.0661392829293808,1.3952195472505289 +1b,5a,2.468970059597331,0.051477534489767086,3.5464699204684274,0.05302668955575522,-1.0774998608710962,0.07390376419633576,-0.8264598476524214 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b/summaries/dec_09_2025/merck/tnks2_neutral/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/tnks2_neutral/dg_plot.png b/summaries/dec_09_2025/merck/tnks2_neutral/dg_plot.png new file mode 100644 index 0000000..d6581c0 Binary files /dev/null and b/summaries/dec_09_2025/merck/tnks2_neutral/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/tnks2_neutral/dg_results.csv b/summaries/dec_09_2025/merck/tnks2_neutral/dg_results.csv new file mode 100644 index 0000000..5777b42 --- /dev/null +++ b/summaries/dec_09_2025/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,-7.2509561846145,0.046115102553393274,-8.603669024704221 +5c,CC(C)(O)c1ccc(-c2nc3cccc(Cl)c3c(=O)[nH]2)cc1,-10.583711134586714,0.06343308637782868,-10.022270579071401 +5d,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.637348967430222,0.044134215880287736,-10.952673772248907 +1b,COc1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-9.370355360734305,0.04563675955882876,-9.99888857195475 +5a,CC(C)(O)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-10.517547486408025,0.029996128286951262,-10.825348419607172 +5b,CC(C)(O)c1ccc(-c2nc3cccc(F)c3c(=O)[nH]2)cc1,-11.257470359958353,0.02537828667746018,-10.539443848422694 +3a,CC(C)(C)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-11.376870098611153,0.04832537027174301,-11.064783886058404 +3b,CC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-11.064209899854301,0.0465525361080105,-11.590833221531327 +5j,CC(C)(O)c1ccc(-c2nc3ccc(F)c(F)c3c(=O)[nH]2)cc1,-11.211937042782752,0.03942290603852206,-11.153266663063665 +5k,CC(C)(O)c1ccc(-c2nc3c(F)cc(F)cc3c(=O)[nH]2)cc1,-11.17611370158798,0.045364600286069694,-11.03146992588755 +5n,CC(C)(OCCO)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.44474388126708,0.0577651572885501,-10.781167858036888 +5p,COCCOC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.760121019212601,0.0507339996076028,-10.568530825025436 +7,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)nc1,-8.242778558823057,0.04516265630120813,-8.448957594650189 +5h,COc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-10.334709479121049,0.04655098691061616,-10.1121858712117 +5m,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.445734630832467,0.05048826249626469,-12.767710766284315 +5e,CC(C)(O)c1ccc(-c2nc3ccc(Cl)cc3c(=O)[nH]2)cc1,-9.5724753302537,0.04279911720197046,-10.170394486166767 +5i,Cc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.845596526434148,0.04320413008833909,-12.153887951643345 +5f,CC(C)(O)c1ccc(-c2nc3c(F)cccc3c(=O)[nH]2)cc1,-11.355533849920135,0.036597371555134324,-10.326806815411242 +5g,CC(C)(O)c1ccc(-c2nc3c(Cl)cccc3c(=O)[nH]2)cc1,-12.11787730816895,0.04273459952922695,-10.873067061365276 +5l,CC(C)(O)c1ccc(-c2nc3c(F)ccc(F)c3c(=O)[nH]2)cc1,-11.899134785243993,0.03914530623702764,-10.155300901199226 +5o,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)OCCO)cc3)nc12,-11.788189270542894,0.05645250665035754,-12.112756832843909 diff --git a/summaries/dec_09_2025/merck/tnks2_positive/README.md b/summaries/dec_09_2025/merck/tnks2_positive/README.md new file mode 100644 index 0000000..5bb4385 --- /dev/null +++ b/summaries/dec_09_2025/merck/tnks2_positive/README.md @@ -0,0 +1,38 @@ +# Tnks2 Positive Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.93 +- RMSE: 1.01 +- R²: 0.07 +- Kendall 𝜏: 0.20 +- Spearman ρ: 0.26 + +## System Details +- Ligands: 6 +- Host Atoms: 4074 +- Map Details: + - Edges: 9 + - Min Dummy Atoms: 3 + - Max Dummy Atoms: 18 + - Mean Dummy Atoms: 8.1 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) +- GPU: RTX 5090, RTX 5080 +- MPS Processes: 12 +- Total Wallclock Time: 1.68 Hours +- Total Nanoseconds Simulated: 1210.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 912 + - 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/dec_09_2025/merck/tnks2_positive/ddg_results.csv b/summaries/dec_09_2025/merck/tnks2_positive/ddg_results.csv new file mode 100644 index 0000000..2c588f7 --- /dev/null +++ b/summaries/dec_09_2025/merck/tnks2_positive/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,0.5788790450455409,0.04980350860127484,-0.5719588464061602,0.051257793215355736,1.150837891451701,0.07146853037740056,1.1309960839922617 +8b,8d,-10.362677737827793,0.06491233370132375,-9.897843486918083,0.06332192724605516,-0.46483425090970953,0.09068228899132794,-0.563054730112017 +8c,8a,13.537771928565526,0.08604989049292876,12.027298046198782,0.08785662617144475,1.5104738823667434,0.12297711338323901,-0.6871869055329446 +8d,8c,0.8015273198106806,0.08460677103933426,0.7492600088188373,0.08308390107109506,0.05226731099184332,0.11858010087233793,2.381237719637223 +8d,8f,9.832240252194108,0.05628931749089381,9.38052029080227,0.05760869573361803,0.4517199613918386,0.08054346086256305,0.6826875274826852 +8e,8b,0.7628370666957378,0.052302645068547496,-0.1774131000625472,0.053042161730675386,0.940250166758285,0.074491862657807,-1.6968044668607012 +8e,8c,-9.885858024785602,0.0841473284389889,-10.029183881125356,0.08424685232744769,0.14332585633975442,0.11907268792843238,0.12137852266450505 +8e,8f,-1.369749907835192,0.03332500967310093,-0.7374087597963446,0.032515851848588295,-0.6323411480388474,0.04656003534310958,-1.5771716694900328 +8f,8a,2.374559583863547,0.06026049835181331,-0.083324178580627,0.061344376280621817,2.4578837624441743,0.08599104699250622,1.0113632866215934 diff --git a/summaries/dec_09_2025/merck/tnks2_positive/dg_comparison_plot.png b/summaries/dec_09_2025/merck/tnks2_positive/dg_comparison_plot.png new file mode 100644 index 0000000..6cd6ed4 Binary files /dev/null and b/summaries/dec_09_2025/merck/tnks2_positive/dg_comparison_plot.png differ diff --git a/summaries/dec_09_2025/merck/tnks2_positive/dg_plot.png b/summaries/dec_09_2025/merck/tnks2_positive/dg_plot.png new file mode 100644 index 0000000..19882f7 Binary files /dev/null and b/summaries/dec_09_2025/merck/tnks2_positive/dg_plot.png differ diff --git a/summaries/dec_09_2025/merck/tnks2_positive/dg_results.csv b/summaries/dec_09_2025/merck/tnks2_positive/dg_results.csv new file mode 100644 index 0000000..69aeaef --- /dev/null +++ b/summaries/dec_09_2025/merck/tnks2_positive/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,-10.949775492841484,0.042009502161457525,-12.004063145357538 +8a,C[NH+]1CCN(c2ccc(-c3nc4ccc(F)cc4c(=O)[nH]3)cc2)CC1,-9.769478511528146,0.04206432765186945,-10.873067061365276 +8d,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C4CC[NH2+]CC4)cc3)nc12,-11.937544655584299,0.04774455282754625,-12.567117875469554 +8c,O=c1[nH]c(-c2ccc(C3CC[NH2+]CC3)cc2)nc2c(F)cc(F)cc12,-11.536667915223548,0.06171772017407306,-10.185880155832331 +8f,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc([C@H]4CC[N@H+](C)CC4)cc3)nc12,-12.059195375052159,0.038040071891278164,-11.88443034798687 +8e,C[N@H+]1CC[C@H](c2ccc(-c3nc4c(F)cc(F)cc4c(=O)[nH]3)cc2)CC1,-11.56915531427877,0.035843932083667186,-10.307258678496837