diff --git a/summaries/dec_08_2025/README.md b/summaries/dec_08_2025/README.md new file mode 100644 index 0000000..67e422c --- /dev/null +++ b/summaries/dec_08_2025/README.md @@ -0,0 +1,13 @@ +# Summary Dec 08 2025 +- Number of Datasets: 19 +- Number of Ligands: 476 +- Number of Edges: 843 +- Total Wallclock Time: 227.69 Hours +- Average Time Per Edge: 0.27 Hours +- TMD Sha: [c1f675e11c1e05722eb072dcd5938757baab1a6b](https://github.com/tmd-industries/tmd/tree/c1f675e11c1e05722eb072dcd5938757baab1a6b) + +## Notes: +- Total naonseconds simulated value fixed for datasets +- Hif2a Ligand 35 still has an incorrect experimental [label](https://chemrxiv.org/engage/chemrxiv/article-details/65281c688bab5d205536cc7b). +- Solvent leg 43 -> 37 in the CDK8 set was unstable +- Added the MALT1 Dataset from https://pubs.acs.org/doi/10.1021/acs.jctc.3c00282, does not yet exclude the six compounds that were outside of the assay limit as described in section 5.3 diff --git a/summaries/dec_08_2025/jacs/cdk2/README.md b/summaries/dec_08_2025/jacs/cdk2/README.md new file mode 100644 index 0000000..00ef83e --- /dev/null +++ b/summaries/dec_08_2025/jacs/cdk2/README.md @@ -0,0 +1,38 @@ +# Cdk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.73 +- RMSE: 0.94 +- R²: 0.57 +- Kendall 𝜏: 0.63 +- Spearman ρ: 0.82 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.43 Hours +- Total Nanoseconds Simulated: 3370.40 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/jacs/cdk2/ddg_results.csv b/summaries/dec_08_2025/jacs/cdk2/ddg_results.csv new file mode 100644 index 0000000..9e6060d --- /dev/null +++ b/summaries/dec_08_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,-53.25958622929969,0.04323612962265282,-51.034790810929366,0.04291353294700715,-2.2247954183703236,0.06091743769021071,-2.04 +1h1r,1h1q,2.8135153876926045,0.05527303259077136,1.2086835399294553,0.05423718276473161,1.604831847763149,0.07743887993789278,-0.5099999999999998 +1h1r,1oi9,-7.4859705019353076,0.0586491201517957,-6.894913561427525,0.05689498656152104,-0.5910569405077833,0.0817114361054524,-2.070000000000001 +17,20,-4.633884177116584,0.0675433133806861,-3.4178814337250865,0.066288653022314,-1.2160027433914975,0.09463764949508367,-1.6800000000000006 +17,21,2.7365019917933147,0.06573315207282568,2.5098349024374054,0.06372065607347303,0.22666708935590935,0.09154872632572811,-0.7899999999999991 +17,26,1.8453207478417284,0.0649270911817702,2.324308442383826,0.06377253281558895,-0.4789876945420975,0.09100803871659509,-1.3900000000000001 +1h1r,1oiu,-52.98814820512204,0.04257030966111195,-50.60545727569509,0.044428179349089145,-2.382690929426948,0.061531247223811356,-1.4100000000000013 +1h1r,20,-2.805713155080143,0.06291852802149467,-3.155707034038428,0.061968820191865094,0.34999387895828515,0.0883112441559019,-1.0500000000000016 +1h1r,26,2.4982744167662774,0.062567702758542,2.6850024980425724,0.06094201190899594,-0.18672808127629495,0.0873421218198726,-0.7600000000000013 +1h1r,21,4.107344050839859,0.06259998270656915,2.8092425168071746,0.059831623380545644,1.2981015340326845,0.08659434733984785,-0.16000000000000036 +1h1s,1oi9,43.74977259509291,0.06831160099649704,42.844629592308664,0.06673393924109684,0.9051430027842382,0.09549813337096712,1.5099999999999991 +1h1s,29,38.42880290121898,0.061766792297190024,38.07412952145128,0.059953753378034325,0.3546733797676961,0.08607897057236671,1.369999999999999 +1h1s,1oiy,30.024822600037226,0.06437734467881802,28.558547239400657,0.06316729810018946,1.466275360636569,0.09019174051526857,1.4600000000000002 +1h1s,31,34.75503357274668,0.05330744857488261,31.964699558173315,0.0511019527349511,2.7903340145733693,0.07384506514919552,1.71 +1h1s,32,11.080993956489609,0.052138791136326176,8.886814647260385,0.050254143410452895,2.1941793092292246,0.07241500169906655,1.4999999999999991 +21,20,-7.346981942119225,0.04957555624643723,-5.216453211616435,0.04621173309451438,-2.13052873050279,0.06777359406688048,-0.8900000000000013 +1oiu,1h1q,55.32695496651203,0.06209615066143581,51.942578957085125,0.062437282970929195,3.3843760094269055,0.08805876578603415,0.9000000000000015 +1oiy,31,3.252385881920729,0.06624976526573775,2.437004814804084,0.06539335568295167,0.815381067116645,0.0930877132882873,0.24999999999999983 +22,1h1q,-0.5333237940705634,0.060497578791004626,0.6322265736506996,0.05842982019317515,-1.165550367721263,0.08410708012635199,-0.31999999999999906 +22,1h1r,-3.8964523578542716,0.06872369974187893,-0.7029369161520523,0.06622945788271987,-3.1935154417022193,0.09544259006151758,0.19000000000000075 +26,1oi9,-9.252536360702297,0.05597394896435357,-8.642498735001467,0.05447728189400813,-0.610037625700831,0.0781079842604025,-1.31 +22,32,-46.702351064876716,0.0665391532602657,-42.76984684456303,0.06695914467520055,-3.9325042203136946,0.09439801889990894,-1.8900000000000008 +28,1h1s,-18.90584947092612,0.05543151437067858,-19.427553843751873,0.05510058522551867,0.5217043728257525,0.07815834745963729,-0.14000000000000012 +28,30,5.676417338382954,0.05460753739518206,3.867897696747463,0.053877454780565395,1.8085196416354918,0.07671221072292256,1.2999999999999998 +28,1oiy,10.0053544191584,0.06679761647041615,8.965111013444517,0.06764696217947368,1.0402434057138823,0.095068570296602,1.32 +30,31,11.335729617702523,0.0442184412854809,10.509775828225873,0.04338667104434022,0.8259537894766484,0.06194896104074153,0.2700000000000001 +30,29,15.99752867010791,0.06129734642601544,16.440862308572203,0.060190456216339255,-0.4433336384642948,0.08590841459602197,-0.07000000000000091 +29,1oi9,4.703924324529492,0.07279354504347456,4.043419278280076,0.06950514483558519,0.6605050462494156,0.10064723224516425,0.14000000000000012 +30,32,-14.405823838829322,0.060317517369203454,-14.536733039858825,0.05782336795761358,0.13090920102950307,0.08355683564823248,0.05999999999999908 diff --git a/summaries/dec_08_2025/jacs/cdk2/dg_plot.png b/summaries/dec_08_2025/jacs/cdk2/dg_plot.png new file mode 100644 index 0000000..99f767b Binary files /dev/null and b/summaries/dec_08_2025/jacs/cdk2/dg_plot.png differ diff --git a/summaries/dec_08_2025/jacs/cdk2/dg_results.csv b/summaries/dec_08_2025/jacs/cdk2/dg_results.csv new file mode 100644 index 0000000..f3a7406 --- /dev/null +++ b/summaries/dec_08_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,-8.314570150240892,0.053965269031516334,-7.04 +1oiu,NS(=O)(=O)c1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-10.816536410559387,0.05739966840829779,-9.08 +1h1r,Clc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-8.847290764815943,0.04032405251262534,-7.669999999999999 +1h1q,c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-7.164552611950275,0.05425841884225685,-8.18 +1oi9,Oc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.661064504453552,0.04785539511438945,-9.74 +20,OCc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-9.291522116195683,0.06041287043259443,-8.72 +21,COc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-7.506165779729421,0.06329592086554911,-7.829999999999999 +26,COc1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.970890062986888,0.051364278078947834,-8.43 +1h1s,NS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.01445148362572,0.04941029632100202,-11.25 +29,CN(C)S(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-10.294646670785228,0.052513833240080306,-9.88 +1oiy,NC(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.69479339613559,0.061611135884265956,-9.79 +31,C[S@](=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-8.554008182450998,0.05746321574641152,-9.54 +32,COc1cc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)ccc1S(N)(=O)=O,-9.181184215056696,0.05093677241558164,-9.75 +22,CSc1cccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)c1,-5.662972771543924,0.05657147357993374,-7.86 +28,CNS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-11.237338820335486,0.05717004699248691,-11.11 +30,CS(=O)(=O)c1ccc(Nc2nc(OCC3CCCCC3)c3nc[nH]c3n2)cc1,-9.468012059134303,0.05364221261365282,-9.81 diff --git a/summaries/dec_08_2025/jacs/mcl1/README.md b/summaries/dec_08_2025/jacs/mcl1/README.md new file mode 100644 index 0000000..b7ca7e1 --- /dev/null +++ b/summaries/dec_08_2025/jacs/mcl1/README.md @@ -0,0 +1,38 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.72 +- RMSE: 2.20 +- R²: 0.08 +- Kendall 𝜏: 0.24 +- Spearman ρ: 0.33 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 30.61 Hours +- Total Nanoseconds Simulated: 16195.00 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/jacs/mcl1/ddg_results.csv b/summaries/dec_08_2025/jacs/mcl1/ddg_results.csv new file mode 100644 index 0000000..49bbdc3 --- /dev/null +++ b/summaries/dec_08_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,-5.704120479245934,0.05341364513392595,-6.45378492740239,0.05236144733177801,0.7496644481564563,0.07479798562241856,-0.0699999999999992 +23 flip,66 flip,-1.5277152458023349,0.05355134521669375,-0.25462416243427377,0.05427307122336544,-1.273091083368061,0.0762450840024064,0.4000000000000001 +23 flip,64 flip,-2.531046081354255,0.053788172940979755,-1.5855904597942934,0.05277382435241326,-0.9454556215599617,0.07535412453945778,-0.6700000000000002 +23 flip,68 flip,4.876290894071595,0.05995209071759239,5.411527786967226,0.06031779059825299,-0.53523689289563,0.08504404179050479,1.1399999999999995 +23 flip,51 flip,-3.5921550846077537,0.06232310898898445,-3.7669600483289325,0.06352499308433941,0.17480496372117885,0.08899210448359003,0.3800000000000015 +23 flip,44 flip,-9.243866344015569,0.06562993479574307,-7.9288634032934855,0.06520159858902551,-1.3150029407220818,0.09251236025449736,0.16000000000000036 +23,42,-5.774597840912437,0.05459710586417366,-6.392035898322907,0.054951954099126996,0.6174380574104694,0.07746328955096309,-0.0699999999999992 +23,64,-2.146549891298741,0.05301962992106337,-0.9057248618946965,0.053059418463482055,-1.2408250294040446,0.0750092197309732,-0.6700000000000002 +23,44,-7.0333132815327515,0.06377449163351509,-7.392074592362785,0.0651461733673881,0.35876131083003354,0.09116583618618913,0.16000000000000036 +23,66,-1.5440608162165175,0.05329744389227027,-0.28939823257796193,0.055119506898456246,-1.2546625836385554,0.07667318674855417,0.4000000000000001 +23,51,-1.9599509343990658,0.061667297679904975,-3.852999002880155,0.06307509770482693,1.893048068481089,0.08821181073765279,0.3800000000000015 +23,68,6.420526293706079,0.06011223561869685,5.33624930283824,0.06017387395759914,1.0842769908678382,0.08505513493107135,1.1399999999999995 +26 flip,64 flip,-8.951503313369544,0.06005351874126712,-8.797601158698484,0.06015195332308655,-0.15390215467106105,0.0849981329312033,-1.2600000000000011 +26 flip,68 flip,-2.2550440660861146,0.05489637913043855,-1.8590120441880067,0.05229581281378861,-0.396032021898108,0.07581862884204427,0.5499999999999986 +26 flip,66 flip,-8.5328957440367,0.060074219606225714,-7.385695903101155,0.06059917528060635,-1.1471998409355453,0.08532978322946032,-0.19000000000000075 +26,64,-9.00465581271636,0.05892141053662312,-8.11929555147711,0.06070487229303294,-0.8853602612392494,0.08459795588392618,-1.2600000000000011 +26,66,-8.51112208792933,0.06020684106043994,-7.64595396431378,0.06032771341016569,-0.8651681236155487,0.08523084368804619,-0.19000000000000075 +26,68,-0.579452437149932,0.05301000126946347,-1.7826129552355812,0.052094344316079004,1.203160518085649,0.07432281577221568,0.5499999999999986 +27,28 flip,6.4779770940231,0.052531726598106676,3.7098947652994827,0.04848166184859093,2.7680823287236165,0.0714846405529142,-0.49999999999999967 +27,29,10.180043965876004,0.05650479942014724,7.089409121274575,0.0538855185010748,3.090634844601429,0.07807971222821422,-0.8200000000000004 +27,29 flip,9.900519599957954,0.05566536836075482,6.951259250542197,0.05410629666281164,2.9492603494157583,0.07762811715675387,-0.8200000000000004 +27,30 flip,2.2851304231539156,0.04971096127453484,1.7710119597141105,0.04818105353796969,0.5141184634398048,0.06922856051419099,-1.7299999999999995 +27,32,1.2987801598353508,0.04841761867236718,1.8302076484862866,0.04715359770138183,-0.5314274886509359,0.06758496559210873,-0.46 +27,40,13.079301633838314,0.06129439501179562,15.399056130628837,0.057573795102015414,-2.3197544967905235,0.0840936664815543,-1.1299999999999994 +27,40 flip,14.516756658255456,0.0600357829098257,15.579624496899005,0.05781874343211891,-1.0628678386435477,0.08335047883284721,-1.1299999999999994 +27,41,14.383949901117788,0.06153556003706805,15.56519492421722,0.057229678824019324,-1.1812450230994318,0.08403488137301089,-1.0099999999999996 +27,41 flip,12.119299218747974,0.05746206048942395,15.594195878817304,0.05840634514228506,-3.474896660069329,0.08193405609738812,-1.0099999999999996 +27,48,10.385323080535903,0.06068359871994414,6.7922021770813465,0.05990419679059696,3.593120903454557,0.08527022895905564,-0.5400000000000001 +28 flip,29 flip,2.251041948054221,0.04749390652257,2.4873609850506693,0.04676242231709514,-0.2363190369964483,0.06665129629449809,-0.32000000000000073 +27,48 flip,11.357108707877408,0.061490786774066455,6.837662107076698,0.06023000374269506,4.519446600800711,0.08607421337972697,-0.5400000000000001 +28,29,4.95892285354845,0.04892596495258677,2.806704801275885,0.04796530720611763,2.1522180522725645,0.06851584299940407,-0.32000000000000073 +28 flip,42 flip,12.669433776557733,0.06476976630941879,12.280107989856086,0.06286570052498332,0.3893257867016477,0.09026194619147987,-2.28 +28,33,-6.352415285875577,0.06220869058681218,-4.171262045374718,0.061265282792498786,-2.18115324050086,0.08731183230336301,-0.25999999999999995 +28,42,9.85845262233639,0.062295400322385966,12.307125661293314,0.06279370385014461,-2.4486730389569242,0.08845205562645783,-2.28 +30 flip,35 flip,-1.9570335671572867,0.0535522132762553,-0.446593577427075,0.05423998079319774,-1.5104399897302117,0.07622214286696481,-0.9600000000000005 +29 flip,33,-11.673751198778284,0.06590874391143767,-7.081555671023101,0.06365117014100179,-4.592195527755182,0.09162660085533147,0.060000000000000775 +29,33,-11.02995627582254,0.0653108766653547,-7.2506421454822165,0.06438121683509677,-3.779314130340324,0.09170851482804047,0.060000000000000775 +30 flip,36 flip,0.6730986392552034,0.0612154458596402,1.4338269065582556,0.061913236715326024,-0.7607282673030523,0.08706652452212926,-0.3299999999999992 +30 flip,40 flip,11.483425755373112,0.05926631450322605,12.424937180158189,0.05920858834847596,-0.9415114247850765,0.08377441715114817,0.6000000000000001 +30 flip,43 flip,11.102944298832147,0.06311894754620159,11.657068001052032,0.06285903979794048,-0.5541237022198844,0.08908007871381352,0.8199999999999996 +30 flip,38,18.840124070531488,0.07002389615559061,18.667066098770825,0.0678269059507089,0.17305797176066104,0.0974876156424766,0.8300000000000005 +30 flip,46 flip,10.944283931613569,0.06226932734752389,11.811315109045347,0.05869740416760156,-0.8670311774317784,0.08557367810447239,0.24999999999999983 +30 flip,49 flip,1.3050904157190966,0.06417252846422748,2.4492650802255076,0.0649303605029504,-1.144174664506411,0.09129110101502329,-0.5099999999999998 +30 flip,52 flip,-3.4811099202977642,0.0636151798688749,-0.5676307609675795,0.06302504449265153,-2.913479159330185,0.08954913368118092,-1.3800000000000008 +30,36,-1.2747330328515032,0.06139513744853934,1.3882632853295371,0.060643906743777315,-2.6629963181810403,0.08629627064637845,-0.3299999999999992 +30,37,-0.47339222675985715,0.06048879670172193,1.5383101395730587,0.061140126440593835,-2.011702366332916,0.08600586949501787,-1.099999999999999 +30,40,10.157630501169216,0.05897107044842807,12.368618982936667,0.05870149814380857,-2.210988481767451,0.08320728954942005,0.6000000000000001 +30,38 flip,14.103296684312442,0.06935420642948091,18.71707214793024,0.06815966038167029,-4.6137754636178,0.09724065637791471,0.8300000000000005 +30,45,14.187245704215151,0.06262634542360712,15.35783225556204,0.06335811295787774,-1.1705865513468885,0.08908596757458578,-1.099999999999999 +30,46,10.373039645042773,0.06291277901757801,12.087372586290085,0.05986126595521982,-1.7143329412473107,0.0868411706823219,0.24999999999999983 +30,49,1.6030995626125204,0.06481202545124755,2.307552684326307,0.06393999717916092,-0.7044531217137864,0.091043516421348,-0.5099999999999998 +30,52,-3.818320922438156,0.06340274398649472,-0.5374012892958444,0.06392922027519737,-3.280919633142312,0.09003806500592791,-1.3800000000000008 +30,50,3.147032110591607,0.0693060735520322,4.616646379715262,0.06974780074956104,-1.4696142691236556,0.09832643358019327,-1.4800000000000004 +31 flip,36 flip,-1.9792144905413636,0.0596461016966425,-1.4778459619206823,0.05912773821020097,-0.5013685286206813,0.08398658746169105,-0.2599999999999983 +30,53,-2.967543405648014,0.06948079821830093,0.41485782557239514,0.06933911074854655,-3.3824012312204093,0.09816055012300744,-2.1100000000000017 +31 flip,43 flip,9.131054222213148,0.06426221900110604,8.738719313617638,0.061423973581596465,0.39233490859550946,0.08889621657584072,0.8900000000000005 +31 flip,46 flip,8.384405316776522,0.06590378701924288,8.701377571336653,0.06625780515755761,-0.31697225456013134,0.09345269331471721,0.32000000000000073 +31 flip,49 flip,-1.063986078639602,0.0692573091792284,-0.7665124585785698,0.06814382058490988,-0.29747362006103234,0.09716046088124336,-0.4399999999999989 +31 flip,52 flip,-5.438297496842239,0.06722136143176273,-3.3629761341924804,0.06965843753337264,-2.0753213626497584,0.09680397384575931,-1.31 +31,36,-2.507901752222012,0.0605305651405321,-1.4542837183183446,0.05953598964555895,-1.0536180339036676,0.0849027878182354,-0.2599999999999983 +31,45,12.339871378877644,0.0656748935764424,13.729016348459563,0.06540562051333362,-1.3891449695819182,0.09268811596429849,-1.029999999999998 +31,49,-0.4595371778307953,0.06905849903650937,-0.8037909773951,0.0692997049396245,0.34425379956430474,0.09783417293509761,-0.4399999999999989 +32,34,1.0004654037691658,0.04708690022763594,1.741408651487846,0.04624615073682334,-0.7409432477186803,0.06599911083507358,-0.28999999999999954 +33,34,4.4040927501407685,0.037636185479079126,4.431262820552167,0.037228838150295304,-0.027170070411398704,0.05293834949671673,0.01000000000000013 +31,52,-4.752751030608036,0.06854085337979364,-3.4274911518331783,0.06777322631871079,-1.3252598787748582,0.09639013843582528,-1.31 +32,39,19.796039510153527,0.07036845026946081,19.056768323350084,0.0685061151386547,0.7392711868034408,0.09820797627848868,-0.4499999999999999 +33,41,15.962476368189689,0.061051123085025014,15.808331005068082,0.055738741874667756,0.15414536312160834,0.08266829486395443,-0.24999999999999983 +33,40,13.63630383093828,0.07232414863930216,15.843277147163153,0.06646393847523467,-2.2069733162248735,0.09822544270218207,-0.3699999999999997 +33,40 flip,15.348526485906717,0.07001065577601466,15.906488130396774,0.06750670199451037,-0.5579616444900573,0.09725557432025808,-0.3699999999999997 +33,48,10.977011359624793,0.06806684412999472,7.257558999825987,0.06776907553188974,3.7194523597988067,0.09605073070135371,0.21999999999999945 +33,48 flip,12.770554995563398,0.0687993788451462,7.2600466966885,0.06786940986740643,5.510508298874897,0.09664166454085917,0.21999999999999945 +35 flip,49 flip,2.2559144700165636,0.05625254852245034,2.774977759076718,0.05583091986629724,-0.5190632890601548,0.07925554131029283,0.45000000000000073 +34,39,16.772819902537396,0.06219222568563467,16.915685217031168,0.06358960234443903,-0.14286531449377135,0.08894667201226139,-0.16000000000000036 +35 flip,52 flip,-1.6659228537301067,0.05498390275177936,-0.24956716884117658,0.052960841761418236,-1.4163556848889303,0.0763418648049359,-0.4200000000000003 +35,49,3.292092216658341,0.05586922106438526,2.7682552346956943,0.05446060915262154,0.5238369819626466,0.07802132920949088,0.45000000000000073 +35,52,-1.9949819030315343,0.05328683671690198,-0.31558467041016697,0.0538635149470245,-1.6793972326213675,0.07576783756807438,-0.4200000000000003 +35,45,15.04837958956486,0.0715222795272705,15.315031694860393,0.07031418577543667,-0.2666521052955337,0.10029716441674529,-0.1399999999999984 +37,56,11.460434679560118,0.05282701605524975,11.889811374830451,0.05343389342723052,-0.42937669527033323,0.07513903507561329,-0.3100000000000006 +37,60,5.73053143901752,0.05401952149267019,6.2403466827805065,0.054630642381004256,-0.5098152437629864,0.07682848292956353,0.02999999999999869 +36 flip,38,16.085672321865847,0.07479163097493836,15.02531744672844,0.07466037194461128,1.0603548751374055,0.10567856548420336,1.1599999999999997 +36,38 flip,13.616008222312615,0.07507763148038746,15.181186196576054,0.07408032644889087,-1.5651779742634389,0.10547296106338869,1.1599999999999997 +37,58,9.178646436058257,0.0627448475290591,11.400676849840488,0.06323710378256561,-2.222030413782231,0.08908337210867046,-0.46000000000000085 +37,63,3.5034740118995735,0.06211314912960655,5.377181739376564,0.0629154436141936,-1.8737077274769902,0.0884103859281675,-0.11000000000000143 +38 flip,47,-11.074983700565198,0.0712729430084776,-15.239175238716955,0.07047820331975134,4.164191538151757,0.10023477215153385,1.239999999999999 +38,47 flip,-14.763395779912878,0.07125392097724186,-15.285573983186092,0.0693269370296016,0.5221782032732138,0.09941501623264652,1.239999999999999 +42 flip,45 flip,7.325764946411223,0.060150530871046624,8.063979834750826,0.06034748366739219,-0.7382148883396044,0.08520507701454708,-0.04999999999999895 +39,43,-8.543800274241248,0.07214011575918693,-7.7508264725436185,0.07101012555309882,-0.792973801697629,0.10122565995248314,0.0 +41,47 flip,-12.582788571665537,0.0722022100740531,-15.560170134428173,0.07224456642815805,2.9773815627626354,0.10213929957646192,1.3499999999999996 +41 flip,47,-15.18564902639449,0.07523118099170811,-17.60561082850275,0.072966796932185,2.4199618021082627,0.10480402686896086,1.3499999999999996 +42 flip,54 flip,-1.328420622708879,0.05253058255265943,-0.020936874897084113,0.054116890311456126,-1.307483747811795,0.07541949297299698,-0.8799999999999996 +42 flip,57 flip,11.218326758774458,0.05433550215909158,11.64545627600269,0.053591961207098825,-0.42712951722823245,0.07631805226094172,-0.14000000000000012 +43 flip,47 flip,-5.709384393402893,0.039088091910251296,-7.479786157606389,0.037742342424888296,1.770401764203495,0.0543356544167987,1.25 +42,54,-1.621725788505527,0.05465833871188635,-0.31553045438263466,0.05266664067273257,-1.3061953341228925,0.07590328734971907,-0.8799999999999996 +42,57,11.089186655094904,0.05287022289536492,11.743975080335716,0.05325571992820524,-0.6547884252408115,0.07504286890889104,-0.14000000000000012 +42,48,-9.122900562044611,0.0677981869077047,-12.892478695239296,0.06666474118726755,3.769578133194684,0.09508302616943483,2.2399999999999993 +44 flip,45 flip,10.617720227752299,0.0675914857243807,9.380452812561614,0.06723281788434537,1.2372674151906846,0.09533551669288162,-0.27999999999999853 +43,41 flip,9.401632720204667,0.073482892263713,10.411518843770775,0.07354984747271526,-1.0098861235661083,0.10396785810383964,-0.0999999999999996 +44 flip,57 flip,14.982074320173275,0.06616073451384463,12.98963280442671,0.06460168461274786,1.992441515746565,0.09246956497257017,-0.3699999999999997 +43,46,1.8592040360166555,0.07402382299568547,1.8968305225291962,0.07396011057104751,-0.03762648651254055,0.1046404526298417,-0.5699999999999997 +44,54,-0.5166641062166887,0.06361097820184301,1.0392587638044108,0.06384381710262302,-1.5559228700210994,0.09012430044127126,-1.109999999999999 +44,48,-7.019335099910482,0.07521040799775217,-11.869987965434884,0.07448816328913561,4.850652865524402,0.105854106870623,2.01 +44,57,12.272950412083349,0.06408529212840301,13.047668843505697,0.06452244767000244,-0.7747184314223489,0.09093993028648613,-0.3699999999999997 +45 flip,51 flip,-6.171426757400224,0.06881826540860876,-5.312134115468093,0.06823982966442499,-0.8592926419321304,0.09691557153770211,0.49999999999999967 +47 flip,46 flip,5.330241002924045,0.07464417532349794,7.471511636513676,0.07367087627048409,-2.141270633589631,0.1048768369097108,-1.8199999999999998 +47,46,5.762067794713456,0.0751206331071726,7.708512471397848,0.07519795372002802,-1.9464446766843917,0.10629130614543182,-1.8199999999999998 +48 flip,51 flip,13.10813980657474,0.07548924599893027,15.123565954687717,0.07631943499606257,-2.015426148112975,0.10734655290043192,-1.7899999999999985 +48 flip,54 flip,9.846850603009408,0.07552426885817512,12.52946412574166,0.07445765248440445,-2.6826135227322534,0.10605591544110239,-3.1199999999999988 +50,53,-5.067638686230222,0.06446661627923156,-3.9111798107449016,0.06456297232063878,-1.15645887548532,0.09123772251305515,-0.6300000000000013 +50,56,7.474716699432205,0.06278411116862363,9.071561156128192,0.06417856264691599,-1.5968444566959867,0.08978158229090313,0.07000000000000091 +50,58,6.189212503965411,0.07074445403306327,8.841428483636827,0.07020689086685675,-2.652215979671416,0.0996683766378631,-0.07999999999999934 +51 flip,54 flip,-3.442754324714766,0.06393745855941217,-2.689473655642278,0.06387907078022599,-0.7532806690724883,0.09037994407379146,-1.3300000000000003 +51 flip,57 flip,9.914383740495914,0.06407115873409781,9.024281906023255,0.06416267962542777,0.8901018344726594,0.09067503977526142,-0.5900000000000009 +51,54,-5.248995277075933,0.06306308807112414,-2.9657150780497235,0.06448778379308465,-2.2832801990262093,0.09019771247437482,-1.3300000000000003 +51,57,7.598333522802541,0.0640096172086318,9.149953586049632,0.06347844235327862,-1.5516200632470907,0.09014845389020318,-0.5900000000000009 +53,60,8.425678513517646,0.06215044978135439,7.19961806070088,0.06339737658753154,1.226060452816766,0.08878009780466535,1.0400000000000016 +56,58,-2.5116296298604466,0.05334100719550019,-0.4458094476195585,0.05354183830419493,-2.065820182240888,0.07557771826155482,-0.15000000000000024 +60,61,4.1737099671753,0.05430745454340338,2.78147659860643,0.05480704385040358,1.3922333685688704,0.07715641045696649,0.8400000000000006 +60,65,-1.5569027939739426,0.05484261912050742,0.0053098290467261874,0.05396711336337688,-1.5622126230206688,0.076942590265552,0.5099999999999998 +60,67,6.736557144136297,0.04910623468960179,7.20640559094293,0.049608932238281375,-0.46984844680663324,0.0698030690099844,1.3400000000000003 +61,65,-5.41913199557032,0.06400060327711699,-3.0676306281947627,0.06489120800258033,-2.3515013673755574,0.09114244947261985,-0.3300000000000009 +61,67,2.8002863353146945,0.06045609018438577,4.2725079205737115,0.06075923775687467,-1.4722215852590173,0.085712448414329,0.49999999999999967 +62 flip,64 flip,-4.413650103426018,0.06403250565629164,-4.53799004240664,0.0635258784150586,0.12433993898062161,0.09019810978633548,-1.5400000000000014 +62 flip,66 flip,-4.397604850625521,0.06451745106801476,-3.452560692191113,0.06363993378583208,-0.9450441584344089,0.09062308019803107,-0.470000000000001 +62,64,-7.38693051651344,0.06424041096326497,-4.3575282908734145,0.06337108701835079,-3.0294022256400255,0.09023704932352654,-1.5400000000000014 +62 flip,68 flip,2.562633271078441,0.06796519331862687,2.1057735067415257,0.06851957614210709,0.4568597643369152,0.09651010215274013,0.2699999999999984 +62,66,-6.804865273133315,0.06345361690045011,-3.5262521467122974,0.06545129941620029,-3.278613126421017,0.09116048537068124,-0.470000000000001 +62,68,1.3038325321400719,0.06917011923076578,2.134876770367235,0.06849911107543745,-0.8310442382271633,0.0973480026118845,0.2699999999999984 +63,65,0.9784240106201333,0.062486644630568244,0.6679129540348707,0.06279483936118405,0.3105110565852626,0.08858765493895769,0.6499999999999999 +63,67,8.77061991846239,0.06137806903605552,8.104218974220474,0.059841967163357386,0.6664009442419166,0.0857223914305658,1.4800000000000004 diff --git a/summaries/dec_08_2025/jacs/mcl1/dg_plot.png b/summaries/dec_08_2025/jacs/mcl1/dg_plot.png new file mode 100644 index 0000000..e9eff2d Binary files /dev/null and b/summaries/dec_08_2025/jacs/mcl1/dg_plot.png differ diff --git a/summaries/dec_08_2025/jacs/mcl1/dg_results.csv b/summaries/dec_08_2025/jacs/mcl1/dg_results.csv new file mode 100644 index 0000000..6cc87dd --- /dev/null +++ b/summaries/dec_08_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,-4.87354999895946,0.08715845030462636,-8.83 +42 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2ccccc12,-4.000870493831135,0.07609241477548385,-8.9 +66 flip,O=C([O-])c1sc2c(Cl)cccc2c1CCCOc1cccc2ccccc12,-6.346259088702797,0.1174726684152864,-8.43 +64 flip,O=C([O-])c1sc2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-5.598439650875847,0.10906535547888142,-9.5 +68 flip,O=C([O-])c1oc2ccc(Cl)cc2c1CCCOc1cccc2ccccc12,-5.441376249567659,0.1109010090428775,-7.690000000000001 +51 flip,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-4.971514322120158,0.077047205290223,-8.45 +44 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-6.081958939927937,0.10092585733867505,-8.67 +23,O=C([O-])c1sc2ccccc2c1CCCOc1cccc2ccccc12,-9.248342325319499,0.08001732768540346,-8.83 +42,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2ccccc12,-8.575459219491998,0.06728165868528722,-8.9 +64,O=C([O-])c1sc2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-10.433610774274968,0.10485418312302622,-9.5 +44,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-8.711362760707743,0.07870731174351833,-8.67 +66,O=C([O-])c1sc2c(Cl)cccc2c1CCCOc1cccc2ccccc12,-10.502113002420996,0.09622110655104035,-8.43 +51,O=C([O-])c1[nH]c2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-7.594049400398326,0.0900140003938906,-8.45 +68,O=C([O-])c1oc2ccc(Cl)cc2c1CCCOc1cccc2ccccc12,-8.23659724852088,0.09333712433221833,-7.690000000000001 +26 flip,O=C([O-])c1oc2ccccc2c1CCCOc1cccc2ccccc12,-5.215152868531573,0.11487672922035065,-8.24 +26,O=C([O-])c1oc2ccccc2c1CCCOc1cccc2ccccc12,-9.532040339217188,0.10152045121191286,-8.24 +27,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1,-7.441746386247754,0.03583544076691717,-6.12 +28 flip,Cc1ccccc1OCCCc1c(C(=O)[O-])[nH]c2ccccc12,-4.390220620148694,0.061762251035691114,-6.62 +29,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1C(F)(F)F,-4.312635370905824,0.05310812540961786,-6.94 +29 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccccc1C(F)(F)F,-4.380143043726128,0.05458459209338284,-6.94 +30 flip,Cc1cccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)c1,-7.075109558394974,0.053599980922605386,-7.85 +32,Cc1ccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc1,-8.042444422668565,0.0492428178453486,-6.58 +40,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(Oc2ccccc2)c1,-10.099222173813649,0.05858447471884154,-7.25 +40 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(Oc2ccccc2)c1,-8.436091425673842,0.056224863696218506,-7.25 +41,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Oc2ccccc2)cc1,-8.50671643190989,0.05532372487409309,-7.13 +41 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Oc2ccccc2)cc1,-10.64028768987267,0.06709772131760797,-7.13 +48,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2[nH]ccc12,-4.2787339667796145,0.0588406989571647,-6.66 +48 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2[nH]ccc12,-2.8857584414478397,0.05401681683664552,-6.66 +28,Cc1ccccc1OCCCc1c(C(=O)[O-])[nH]c2ccccc12,-6.291093745891891,0.06401806818156307,-6.62 +33,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)cc1,-8.350174195725504,0.03897222924858272,-6.88 +35 flip,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-8.326201408181973,0.07555691495893149,-8.81 +36 flip,CCc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-8.006065390924029,0.07094637733263996,-8.18 +43 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ccccc2c1,-7.5664948306447855,0.07189122060870018,-7.03 +38,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(-c2ccccc2)c1,-6.727893118153128,0.07359347485950979,-7.02 +46 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2c(c1)CCC2,-8.009135971611657,0.07643286314753439,-7.6 +49 flip,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)ccc1Cl,-8.444728624313623,0.0853316749412273,-8.36 +52 flip,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)ccc1Cl,-9.854021136619338,0.0759862672999921,-9.23 +30,Cc1cccc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)c1,-7.890271691961384,0.061449173118940416,-7.85 +36,CCc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-10.405745438044256,0.08010861295956002,-8.18 +37,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)cc(C)c1Cl,-9.930573905284566,0.08202089061370371,-8.95 +38 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(-c2ccccc2)c1,-12.227608813798131,0.08682298216676242,-7.02 +45,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2c1CCCC2,-9.652976909375182,0.09031336507530228,-8.95 +46,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2c(c1)CCC2,-9.653288284814762,0.07284005035708359,-7.6 +49,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)ccc1Cl,-8.667328581075829,0.08464701259217183,-8.36 +52,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)ccc1Cl,-10.842988467047245,0.07966932096439268,-9.23 +50,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cccc(Cl)c23)cc(C)c1Cl,-9.470195258624932,0.08314630560319028,-9.33 +31 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(C(F)(F)F)c1,-7.800668703427622,0.07548784356407844,-7.920000000000001 +53,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3cc(Cl)ccc23)cc(C)c1Cl,-11.125480756153207,0.08339901104629928,-9.96 +31,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc(C(F)(F)F)c1,-9.043003647166532,0.08193227730051822,-7.920000000000001 +34,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(C(F)(F)F)cc1,-8.449385814347435,0.05511952999758771,-6.87 +39,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(-c2ccccc2)cc1,-8.188986538743997,0.06493386017442643,-7.03 +35,Cc1cc(OCCCc2c(C(=O)[O-])[nH]c3ccccc23)ccc1Cl,-9.224501885296407,0.08590522794848932,-8.81 +56,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3ccccc23)cc(C)c1Cl,-10.508497239789966,0.08889962989898467,-9.26 +60,Cc1cc(OCCCc2c(C(=O)[O-])sc3ccccc23)cc(C)c1Cl,-10.251331297579581,0.09296184881123983,-8.92 +58,Cc1cc(OCCCc2c(C(=O)[O-])n(C)c3cc(Cl)ccc23)cc(C)c1Cl,-12.328809597293368,0.09520546275189196,-9.41 +63,Cc1cc(OCCCc2c(C(=O)[O-])sc3cc(Cl)ccc23)cc(C)c1Cl,-11.705650793946983,0.1019638269877902,-9.06 +47,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ncccc2c1,-8.001515907997845,0.08642079878364971,-5.78 +47 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ncccc2c1,-5.831839306917576,0.0645993676426987,-5.78 +45 flip,O=C([O-])c1[nH]c2ccccc2c1CCCOc1cccc2c1CCCC2,-4.583480167538248,0.09222607318496404,-8.95 +43,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc2ccccc2c1,-9.40075739036932,0.07057705321524964,-7.03 +54 flip,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-5.499756895994657,0.08476961820002472,-9.78 +57 flip,Cn1c(C(=O)[O-])c(CCCOc2cccc3ccccc23)c2ccccc21,-4.228764495212701,0.08422608969818582,-9.04 +54,O=C([O-])c1[nH]c2cc(Cl)ccc2c1CCCOc1cccc2ccccc12,-9.993535994759126,0.07839141388872055,-9.78 +57,Cn1c(C(=O)[O-])c(CCCOc2cccc3ccccc23)c2ccccc21,-9.278943671669007,0.08302540822425805,-9.04 +61,Cc1cc(OCCCc2c(C(=O)[O-])sc3cccc(Cl)c23)cc(C)c1Cl,-9.10558679903175,0.10288427707675452,-8.08 +65,Cc1cc(OCCCc2c(C(=O)[O-])sc3c(Cl)cccc23)cc(C)c1Cl,-11.582632154351916,0.09887462780935763,-8.41 +67,Cc1cc(OCCCc2c(C(=O)[O-])oc3ccccc23)cc(C)c1Cl,-10.770965185198534,0.10385871575394161,-7.58 +62 flip,O=C([O-])c1sc2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-5.6650656429225394,0.12471323910497552,-7.959999999999999 +62,O=C([O-])c1sc2cccc(Cl)c2c1CCCOc1cccc2ccccc12,-7.342248127741919,0.09320053577404819,-7.959999999999999 diff --git a/summaries/dec_08_2025/jacs/p38/README.md b/summaries/dec_08_2025/jacs/p38/README.md new file mode 100644 index 0000000..e5c33b1 --- /dev/null +++ b/summaries/dec_08_2025/jacs/p38/README.md @@ -0,0 +1,38 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.09 +- RMSE: 1.42 +- R²: 0.35 +- Kendall 𝜏: 0.47 +- Spearman ρ: 0.64 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 18.97 Hours +- Total Nanoseconds Simulated: 8308.80 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/jacs/p38/ddg_results.csv b/summaries/dec_08_2025/jacs/p38/ddg_results.csv new file mode 100644 index 0000000..5b3f730 --- /dev/null +++ b/summaries/dec_08_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,3flw,18.731479698364733,0.0637092635332887,20.947432697650413,0.06436590523231768,-2.21595299928568,0.0905640106020583,-1.4099999999999995 +2aa,2v,11.832304228121698,0.0631604795280806,11.52064150922787,0.0634941006896874,0.3116627188938277,0.0895586232398045,0.29999999999999877 +2aa,2y,-13.381736851286915,0.06769732044933448,-14.101030759719993,0.06599417765771196,0.7192939084330782,0.0945418356112125,-0.5099999999999998 +2aa,3fmh,15.876901778276366,0.06640976210395791,17.581997992670928,0.06334237306990845,-1.7050962143945607,0.09177424872387539,-1.5599999999999998 +2aa,2z,6.829748044652754,0.06429995269237415,8.206634161068436,0.06481941415266733,-1.3768861164156816,0.09130191874947953,-1.0900000000000005 +2aa,3flq,-9.228124182709909,0.06966472425862603,-8.392891924533883,0.06913620918161205,-0.8352322581760261,0.09814779277209454,-0.66 +2aa,3fmk,14.931580191023352,0.06322084887215541,18.103333408085614,0.06361134426180433,-3.171753217062263,0.08968432890371485,-2.560000000000001 +2bb,3fly,27.54543831827547,0.0702974841437698,28.058162916869367,0.06739478441706945,-0.5127245985938981,0.09738476905331159,-2.36 +2c,3flz,3.567518425215344,0.07068850627114853,2.8736277665851917,0.06868947375380331,0.6938906586301522,0.09856525109500122,0.9700000000000006 +2e,2n,-1.4612080452974185,0.059857853867263194,1.2644671176104139,0.06116297432597778,-2.7256751629078324,0.0855796243155744,-1.1499999999999997 +2e,3flz,-0.28519478326233494,0.039176347594409494,1.0389417111175043,0.03886068074046167,-1.3241364943798393,0.05518096337007975,1.2099999999999986 +2e,2m,-14.189154492311394,0.06492973878560483,-11.48626243879658,0.06366350201602528,-2.702892053514814,0.09093356073371003,-0.2600000000000017 +2e,2r,-3.780546239203689,0.06362891111001441,-2.3007504713226323,0.06481255989791465,-1.4797957678810572,0.09082569157219168,-0.08999999999999947 +2ee,2e,-5.334581752766516,0.05760969201607984,-6.302101589686175,0.057170153065089824,0.9675198369196584,0.08116220189024798,1.5599999999999998 +2ee,2f,-7.745525577973094,0.06276363917599077,-7.960648755931654,0.06093976438888983,0.21512317795855948,0.08748102243565384,3.779999999999998 +2f,2c,-1.2398474482042103,0.0730882530012008,-0.4858585847492475,0.07085128732940728,-0.7539888634549627,0.1017929154853213,-1.9800000000000002 +2f,2ff,5.812293243611713,0.06842628184563361,3.9406192255601638,0.06846772354206529,1.87167401805155,0.09679868394896063,-2.9599999999999977 +2f,2k,-9.754771646560025,0.061687709192719486,-10.64580543538347,0.06250079699916,0.8910337888234462,0.08781641697869332,-2.07 +2f,3fln,2.4343399424700984,0.04870589340102837,2.5960414884028453,0.04908676439271885,-0.1617015459327465,0.06915037592478172,-2.4000000000000004 +2f,2m,-10.962605675498185,0.06858326669457745,-9.603898050778065,0.0690957390644661,-1.3587076247201197,0.09735443301341919,-2.48 +2f,3flz,2.044958518008202,0.03851066659143587,2.772076251746634,0.038496299080977014,-0.7271177337384319,0.054452148573300274,-1.0099999999999996 +2g,2i,-5.834756692294517,0.04479621571429467,-7.817156060312809,0.04543272711529605,1.9823993680182914,0.06380308484277683,0.6099999999999994 +2g,2gg,-25.080131425721095,0.058237267795075924,-29.159560697947057,0.06044703265830782,4.079429272225961,0.08393701875471822,0.0 +2ff,2x,-0.14963783127457125,0.06775979101523866,0.5754420383714149,0.06715802008493804,-0.7250798696459863,0.09540224808754645,1.2099999999999986 +2g,2j,-8.791757294367102,0.04855899627946035,-10.578380385074068,0.050420401982009484,1.7866230907069665,0.07000137895567536,0.5800000000000007 +2ff,3fly,-13.178638104365309,0.06620738091242798,-11.945466597811723,0.0629426473494553,-1.2331715065535849,0.09135203414616024,0.01999999999999856 +2g,3fln,-1.4824197335692344,0.039827560241026745,-2.4449054177729823,0.03876917438040268,0.9624856842037479,0.05558132273426646,-0.22000000000000114 +2g,2k,-13.631041840352928,0.0592611696457776,-15.495624243710054,0.05829246497783081,1.8645824033571254,0.08312579443817222,0.10999999999999972 +2g,2m,-15.206927585190027,0.062477253704330285,-14.472484358951366,0.06398380577766742,-0.7344432262386604,0.0894278179999351,-0.3000000000000005 +2g,2x,1.1560031733039895,0.06507454217429959,-0.529683436681191,0.06396266586726455,1.6856866099851806,0.09124647206353802,0.4300000000000005 +2gg,2ee,27.91282474025925,0.06452101080078419,32.156098196033284,0.06273456926311555,-4.243273455774033,0.08999214974309455,-1.5999999999999985 +2h,2e,5.650541906783296,0.057926736062351325,9.00396097138651,0.05743114034182113,-3.353419064603214,0.08157108943614316,-1.2199999999999989 +2h,3fln,5.235382241016384,0.0551127372251813,9.670437721516203,0.05606916894878264,-4.435055480499818,0.07862038864734144,-1.4000000000000012 +2h,2k,-6.439369697083714,0.06592174077707637,-3.396257069492917,0.0646879902486139,-3.0431126275907974,0.09235914675593761,-1.0700000000000003 +2gg,3fmk,19.067511639040433,0.07621574407718767,24.592846612546683,0.07517590208115836,-5.525334973506253,0.10705258473738631,-1.17 +2j,2e,6.769375349620182,0.048898279069721814,7.206119114295207,0.04915246501509422,-0.4367437646750249,0.06933257901622047,-0.6199999999999996 +2j,2i,2.327197017823314,0.03944476545422608,2.52330447726,0.03884975435726159,-0.1961074594366858,0.05536418459038726,0.02999999999999869 +2i,2c,0.4381206621311577,0.07400737410412296,2.4013813838517692,0.07256476553166907,-1.9632607217206113,0.10364717371184666,-0.4100000000000002 +2l,2t,-13.820467426683214,0.052358945555610575,-12.662597146902158,0.05161147914488109,-1.1578702797810565,0.07352009221442725,0.4100000000000002 +2l,2q,-13.7297011440338,0.07006631376168905,-10.91645811624354,0.07334446099202423,-2.8132430277902616,0.10143322080246699,0.0 +2n,2r,-4.654332140013424,0.06418660196714523,-5.731929044515663,0.06338633781100816,1.0775969045022393,0.09020946565178167,1.06 +2n,2s,-12.74915436596977,0.058175124951204166,-12.706534640196944,0.059407688366445416,-0.04261972577282601,0.08314817256039313,0.7399999999999994 +2l,2u,-6.66952711519394,0.07839892598153834,-4.7319009182309415,0.07582321164460071,-1.9376261969629989,0.10906672736981084,0.0 +2o,2n,29.596770375803942,0.062248494196318276,29.46806723534852,0.061720858074816635,0.12870314045542203,0.08766036362690226,-1.359999999999999 +2n,2u,-0.12815849929536027,0.07314911119926186,1.280011921317847,0.07289651038619123,-1.408170420613207,0.10327000385264863,-0.4100000000000002 +2o,2p,1.2569689569141684,0.062163132261185784,1.3489424538074384,0.06131584335319473,-0.09197349689327002,0.08731487650243337,-0.709999999999999 +2p,2n,29.026160894449642,0.06813145990648733,28.207617886389414,0.06648584979940997,0.8185430080602298,0.09519592455845469,-0.6499999999999999 +2r,2s,-7.552540555485723,0.054723442500163304,-7.275010217978049,0.05485888033202452,-0.2775303375076738,0.0774864627554521,-0.32000000000000073 +2p,2s,19.837723451516453,0.08935826788447311,17.516377875132385,0.07988721486394966,2.321345576384071,0.1198618669053345,0.08999999999999947 +2q,2n,11.532218357476415,0.07638956232031557,8.861522840263548,0.07660328108887403,2.6706955172128675,0.1081823826002664,0.4100000000000002 +2t,2f,9.531108340779676,0.057721294861250126,7.122384656404219,0.058989578000255824,2.408723684375458,0.08253192226713034,3.369999999999998 +2q,2o,-19.820440863648468,0.07843692885705696,-22.677028768267405,0.07871426902972864,2.8565879046189386,0.11112285074372197,1.7699999999999991 +2v,2bb,-25.450402079182368,0.06308093842470615,-24.514597169466068,0.062027163873906,-0.935804909716299,0.08846792554808752,-0.08999999999999947 +2x,3fmh,-5.0528871433956875,0.06846461412081989,-3.7193715920427923,0.06913628347099976,-1.333515551352895,0.0972996869414039,-0.5999999999999993 +2y,2v,4.5961807257685345,0.058157682721405854,3.660531699937382,0.05752536082305278,0.935649025831152,0.08180148652283847,0.8099999999999986 +2t,2u,8.350984014732619,0.081359087623869,8.53562039909728,0.08267784843042959,-0.18463638436466137,0.11599537818410474,-0.4100000000000002 +2z,3fly,6.434088452643987,0.057262305387372925,6.303486199631875,0.05769657903947718,0.13060225301211173,0.08128878674906764,-1.06 +2z,2bb,-20.587952192244344,0.08347238727771897,-20.896795368245026,0.0829661019155241,0.3088431760006796,0.11769032885032922,1.2999999999999998 +3flq,3fly,23.16193824395875,0.06474421770660163,22.87208163208742,0.0630600762623397,0.2898566118713326,0.09037912892173683,-1.4900000000000007 +3flq,2y,16.387783885383612,0.07728761149427114,16.044665522604067,0.07599977706907318,0.3431183627795487,0.10839437718368151,0.15000000000000024 +3fmh,3fly,-2.231256420916083,0.054878322769944594,-3.050713026905015,0.053764961388074926,0.819456605988932,0.07682643674610587,-0.5900000000000009 +3flw,2x,8.332472958548966,0.07109156261805628,6.027327255539652,0.07080081459367338,2.305145703009313,0.10033327275936299,0.449999999999999 +3flw,3fly,-3.6903056406257737,0.061922982482718186,-5.1207311227699055,0.06191540231761108,1.4304254821441316,0.08756696182754464,-0.7400000000000011 +3fmk,3fly,-1.6438826361474932,0.05431925515558977,-3.3297594498954224,0.05500011802564821,1.6858768137479292,0.07730196933774261,0.4100000000000002 diff --git a/summaries/dec_08_2025/jacs/p38/dg_plot.png b/summaries/dec_08_2025/jacs/p38/dg_plot.png new file mode 100644 index 0000000..8c1d1fe Binary files /dev/null and b/summaries/dec_08_2025/jacs/p38/dg_plot.png differ diff --git a/summaries/dec_08_2025/jacs/p38/dg_results.csv b/summaries/dec_08_2025/jacs/p38/dg_results.csv new file mode 100644 index 0000000..687c215 --- /dev/null +++ b/summaries/dec_08_2025/jacs/p38/dg_results.csv @@ -0,0 +1,35 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2aa,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CO)CO)nc21,-9.282028091667279,0.05653740802952244,-9.27 +3flw,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CCO)CCO)nc21,-11.631568969408232,0.06458192052423922,-10.68 +2v,CNc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-8.709437991233091,0.08280008527182821,-8.97 +2y,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCC(C)(C)O)nc21,-9.332245657754227,0.07036733978693029,-9.78 +3fmh,C[C@H](Cn1ncnn1)Nc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-10.95658735851983,0.062313144269104045,-10.83 +2z,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(C)(C)CO)nc21,-10.383491514221003,0.07075593520332692,-10.36 +3flq,C[C@@H](CS(C)(=O)=O)Nc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-10.137590985799577,0.06987972374792395,-9.93 +3fmk,C[C@@H](Cn1ncnn1)Nc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-12.169903971916716,0.062496117064078566,-11.83 +2bb,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCCS(C)(=O)=O)nc21,-9.756541587798884,0.07995591598998981,-9.06 +3fly,CC(C)Nc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-10.186323761398471,0.052981643868433195,-11.42 +2c,Cn1c(=O)c(-c2ccccc2Cl)cc2cnc(NC3CCOCC3)nc21,-11.43266200106083,0.06803815963964849,-10.46 +3flz,Cn1c(=O)c(Oc2ccccc2)cc2cnc(NC3CCOCC3)nc21,-11.020754818865603,0.048376962231362085,-9.49 +2e,Cn1c(=O)c(Oc2ccc(F)cc2)cc2cnc(NC3CCOCC3)nc21,-9.623014157166157,0.037864925353324544,-10.7 +2n,O=c1c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc2n1CCCO,-12.122650048320974,0.05426311880067001,-11.85 +2m,O=c1c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc2n1C1CC1,-12.050404169761595,0.057299257469189686,-10.96 +2r,CC(C)(O)Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-11.164354439081986,0.06966920350105499,-10.79 +2ee,CC(=O)N1CCC(Nc2ncc3cc(Oc4ccc(F)cc4F)c(=O)n(C)c3n2)CC1,-10.756051590720736,0.062172213485359284,-12.26 +2f,Cn1c(=O)c(Oc2cccc(F)c2)cc2cnc(NC3CCOCC3)nc21,-10.451370736051064,0.03795163727654503,-8.48 +2ff,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(N[C@H]3CC[C@H](O)CC3)nc21,-8.7796874301229,0.06412998569092368,-11.44 +2k,O=c1[nH]c2nc(NC3CCOCC3)ncc2cc1Oc1ccc(F)cc1F,-9.403211020657968,0.05563881741186287,-10.55 +3fln,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-10.468810032824578,0.04757716369414571,-10.88 +2g,Cn1c(=O)c(Oc2ccccc2F)cc2cnc(NC3CCOCC3)nc21,-11.252291528804669,0.040269636454966944,-10.66 +2i,Cn1c(=O)c(Cc2ccccc2F)cc2cnc(NC3CCOCC3)nc21,-9.39324954198963,0.05282391680579786,-10.05 +2gg,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCS(=O)(=O)CC3)nc21,-6.81104234902339,0.0596491985997457,-10.66 +2x,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(N[C@H]3CCOC3)nc21,-9.509842032465139,0.05659699965125393,-10.23 +2j,Cn1c(=O)c(Cc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-9.26829765477441,0.053844244906628494,-10.08 +2h,Cn1c(=O)c(Sc2ccccc2F)cc2cnc(NC3CCOCC3)nc21,-6.205432765926649,0.06288536935960509,-9.48 +2l,CCn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-11.85986006005949,0.07451285074567922,-12.26 +2t,N#CCn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-13.019502926313224,0.06327108187778165,-11.85 +2q,O=c1c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc2n1C1CCS(=O)(=O)CC1,-14.90676178381273,0.0772030131453438,-12.26 +2s,O=c1c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc2n1C[C@H](O)CO,-11.574701440579416,0.07518766554153429,-11.11 +2u,CS(=O)(=O)N1CCC(n2c(=O)c(Oc3ccc(F)cc3F)cc3cnc(NC4CCOCC4)nc32)CC1,-13.523434538654092,0.07898413749350885,-12.26 +2o,CS(=O)(=O)CCn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-12.450271792875775,0.06477158568753597,-10.49 +2p,CS(=O)(=O)CCCn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC3CCOCC3)nc21,-12.986621250369637,0.07779485652143114,-11.2 diff --git a/summaries/dec_08_2025/jacs/ptp1b/README.md b/summaries/dec_08_2025/jacs/ptp1b/README.md new file mode 100644 index 0000000..4629d18 --- /dev/null +++ b/summaries/dec_08_2025/jacs/ptp1b/README.md @@ -0,0 +1,38 @@ +# Ptp1B Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.97 +- RMSE: 1.66 +- R²: 0.32 +- Kendall 𝜏: 0.53 +- Spearman ρ: 0.67 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 11.71 Hours +- Total Nanoseconds Simulated: 5331.00 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/jacs/ptp1b/ddg_results.csv b/summaries/dec_08_2025/jacs/ptp1b/ddg_results.csv new file mode 100644 index 0000000..b669563 --- /dev/null +++ b/summaries/dec_08_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) +20667,23486,0.21711637323393546,0.031469636756727384,1.1012076737194343,0.03166531468786758,-0.8840913004854988,0.04464336671759927,-1.05 +20667,23485,6.611645038366876,0.04188679467170833,4.168077891135661,0.0413218591300142,2.4435671472312155,0.058838759417841155,0.4100000000000002 +20669,23466,-11.971122067966581,0.06603378891026554,-13.887260365774951,0.0650123830483516,1.9161382978083705,0.09266645146692035,0.7599999999999997 +20670,23483,-5.336637988548126,0.07208796529861465,-3.8626156118300914,0.06897841573860673,-1.4740223767180345,0.09977322576073372,-0.7899999999999984 +20669,23470,-18.938325609156863,0.0714461753763946,-18.024677001381818,0.06987490452142084,-0.9136486077750469,0.09993527033931619,0.8899999999999997 +23466,23468,2.4081479569596937,0.061028351063568444,3.717693124415329,0.06192129910585362,-1.309545167455635,0.08694082422254083,0.0999999999999996 +23330,20670,-26.520430180589745,0.08417994437261261,-27.096642201843594,0.08396710502371954,0.5762120212538483,0.11889801411562978,1.05 +23330,23475,-23.465094891816406,0.08402123171829899,-24.4017973415445,0.0832639181856226,0.9367024497280938,0.1182896760122461,1.4099999999999995 +23467,20669,5.763551786668078,0.06335703354293651,7.381871592621635,0.06032954325360037,-1.6183198059535564,0.08748581307017052,-1.2699999999999996 +23466,23472,-18.281161899534702,0.07513187816812888,-16.655313861258314,0.07177594246852056,-1.6258480382763878,0.10390661689380006,-0.8000000000000002 +23467,23471,-7.908718184813102,0.06027452659652189,-6.2191615910870475,0.05996718645011416,-1.689556593726055,0.08502400841631486,-0.4100000000000002 +23467,23473,8.14846293881883,0.06054933267934185,11.056382818980047,0.05901165139132214,-2.9079198801612187,0.08454937426051447,-1.05 +23467,23472,-19.85331449441745,0.0827918302068743,-19.638319134822925,0.07445209647962105,-0.21499535959452376,0.1113445185862991,-1.31 +23469,23473,3.936195454426382,0.057320681342914875,5.4808501856588645,0.05352966563928085,-1.544654731232482,0.07842885701748556,-0.6700000000000002 +23468,23475,23.872867046583277,0.06493899329709388,25.089469795093677,0.06343818435558093,-1.2166027485103972,0.09078257588751643,-0.9700000000000006 +23469,23468,-18.06614651529524,0.06650520420264813,-18.200603870256476,0.06629754059677764,0.13445735496123715,0.09390583621488766,-0.030000000000000387 +23469,23474,21.3269067645777,0.06956841957488238,21.742626043722993,0.07134794961439626,-0.41571927914529205,0.09965086510575465,-1.3899999999999992 +23470,20670,20.942339923834155,0.0764699390623813,21.776302830558983,0.07356731047911541,-0.8339629067248268,0.10611220830486412,-1.3600000000000005 +23470,23330,48.02984919822495,0.07789534803838785,49.02444939278602,0.07802944480787061,-0.9946001945610642,0.11025551915004572,-2.4100000000000006 +23470,23475,24.369020448879684,0.0739159581835671,24.739416146933657,0.070805434329106,-0.37039569805397365,0.10235711213554329,-1.000000000000001 +23471,23472,-16.61338371165915,0.07784377319088576,-16.456301705361113,0.07781762522619404,-0.15708200629803826,0.11006923194262079,-0.8999999999999998 +23471,23476,35.834521934399135,0.07581285743235895,37.92560880030962,0.07407627410078103,-2.091086865910486,0.10599473447635607,-1.6599999999999995 +23473,23474,16.788163263522016,0.06560374447017076,16.45403886696538,0.06635855386245718,0.3341243965566387,0.09331296243943865,-0.7199999999999991 +23477,23480,4.071069235877365,0.05562843624358474,4.9198515620276595,0.05511708256632413,-0.8487823261502943,0.07830974211124414,0.12999999999999828 +23476,23468,-34.20587694718342,0.0738108700269919,-35.700655342481085,0.072652630525459,1.4947783952976645,0.10356857272556357,1.6599999999999995 +23477,23468,-14.767942139451531,0.06872722078967083,-16.389924801117846,0.06851571091258515,1.6219826616663147,0.09704552292264236,1.099999999999999 +23477,23482,-12.519623382093416,0.05469432881710575,-11.098212925332746,0.055105450717093045,-1.4214104567606711,0.07764071292490594,-1.1600000000000015 +23474,23476,5.515147100859527,0.0853803263095042,6.692122266485384,0.08358296895364709,-1.1769751656258578,0.11948185142448936,-0.3000000000000005 +23480,20670,5.21820261021556,0.061760204939342485,4.341213845690975,0.06017738941338943,0.876988764524585,0.08623016357841554,-0.35999999999999954 +23480,23479,1.191489826581808,0.05777913009760285,0.5112842423219611,0.05526327275292819,0.6802055842598467,0.07995284354042857,-0.4200000000000003 +23482,20667,18.825034407325415,0.059144534427409266,19.714531794303046,0.05892470095531815,-0.8894973869776307,0.08348770170096115,-1.4099999999999995 +23482,23479,16.937597008301125,0.06000301742751781,14.900186222873165,0.06013484546303928,2.0374107854279613,0.08495034867068305,0.8699999999999993 +23482,23483,24.67859654603847,0.07062278781715836,24.954987974977254,0.06968335761680437,-0.2763914289387828,0.09921365071308898,0.14000000000000182 +23482,23486,18.704501528958787,0.06167475515809539,20.78660172705143,0.060698035831778366,-2.0821001980926415,0.08653338649126627,-2.4599999999999995 +23482,23484,17.772343960087575,0.07410396257678406,21.97085092178635,0.07090409686453752,-4.198506961698777,0.10256114382044075,2.2600000000000002 +23484,23485,6.981184897643487,0.053473198178206706,2.084100328036645,0.05195596988720541,4.897084569606842,0.07455739889726548,-3.26 +23485,23486,-5.8996629903640265,0.037713152995640424,-3.0985577012176018,0.037233546543502374,-2.8011052891464248,0.0529964045674774,-1.4600000000000002 +23483,23479,1.0783275296665766,0.06835346044056706,-2.4883759348958003,0.06735681316797165,3.566703464562377,0.09596424247783757,0.7299999999999975 +23484,23486,1.0289115816800072,0.055078434727781685,-0.9598777198229813,0.05369837402185319,1.9887893015029885,0.07692300920175539,-4.72 diff --git a/summaries/dec_08_2025/jacs/ptp1b/dg_plot.png b/summaries/dec_08_2025/jacs/ptp1b/dg_plot.png new file mode 100644 index 0000000..4f2efdb Binary files /dev/null and b/summaries/dec_08_2025/jacs/ptp1b/dg_plot.png differ diff --git a/summaries/dec_08_2025/jacs/ptp1b/dg_results.csv b/summaries/dec_08_2025/jacs/ptp1b/dg_results.csv new file mode 100644 index 0000000..dad1076 --- /dev/null +++ b/summaries/dec_08_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,-11.694442713748558,0.08273173372056057,-11.42 +23486,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Cl,-12.497638331576452,0.08083550283807966,-12.47 +23485,Cc1c(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc(C(=O)[O-])c1OCC(=O)[O-],-9.522989398689237,0.08248518461409182,-11.01 +20669,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCc3ccccc3)c2)c1Br,-7.603730430656762,0.06926198823148591,-8.61 +23466,Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-5.750077283101074,0.0675864577342737,-7.85 +20670,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCC3)c2)c1Br,-9.151552681542482,0.06713956030904689,-9.08 +23483,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)c4ccccc4)CC3)c2)c1Br,-11.169214621039684,0.07701552147117859,-9.87 +23470,CC(C)NC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-8.423127254340821,0.06933054906155715,-7.72 +23468,CCC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.35186190080341,0.05432595251511755,-7.75 +23330,CC1(C)CC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC(C)(C)C1,-9.572297090944957,0.0806459993216534,-10.13 +23475,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCC3)c2)c1Br,-8.659630753035866,0.06977241990954071,-8.72 +23467,COc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-6.001948407165193,0.06700401249665898,-7.34 +23472,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NS(=O)(=O)c3ccc(F)cc3)c2)c1Br,-7.037064025155838,0.07790727841203476,-8.65 +23471,COC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.301174910661225,0.07335886819775443,-7.75 +23473,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(OCc3ccccc3)c2)c1Br,-8.838408297308115,0.07133219223854378,-8.39 +23469,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC(=O)c3ccccc3)c2)c1Br,-7.473079653156246,0.07380204045828141,-7.72 +23474,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCC3CCCCC3)c2)c1Br,-8.163393334019236,0.08351129087337754,-9.11 +23476,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCCC3)c2)c1Br,-9.17622771135351,0.08147960833158177,-9.41 +23477,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCOCC3)c2)c1Br,-8.958545545583672,0.05026249655904816,-8.85 +23480,COC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-9.634549943960172,0.06355824503736845,-8.72 +23482,CS(=O)(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-10.540001877970619,0.07006204875537111,-10.01 +23479,CC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-8.435523458612918,0.07316067633052031,-9.14 +23484,O=C([O-])COc1cc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc1C(=O)[O-],-14.513520375573945,0.08405549011324251,-7.75 diff --git a/summaries/dec_08_2025/jacs/tyk2/README.md b/summaries/dec_08_2025/jacs/tyk2/README.md new file mode 100644 index 0000000..0e934e3 --- /dev/null +++ b/summaries/dec_08_2025/jacs/tyk2/README.md @@ -0,0 +1,38 @@ +# Tyk2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.61 +- RMSE: 0.78 +- R²: 0.62 +- Kendall 𝜏: 0.57 +- Spearman ρ: 0.74 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 5.72 Hours +- Total Nanoseconds Simulated: 2648.00 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/jacs/tyk2/ddg_results.csv b/summaries/dec_08_2025/jacs/tyk2/ddg_results.csv new file mode 100644 index 0000000..e4c0c85 --- /dev/null +++ b/summaries/dec_08_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_50,-3.3168808530171345,0.0418417390633985,-2.907847098380094,0.04174527689656916,-0.4090337546370401,0.05910498516217357,0.5599999999999987 +ejm_43,ejm_42,-1.3532497753878834,0.04862391968851347,-0.9425264242237096,0.04894741204945827,-0.4107233511641738,0.06899372951373524,-1.5199999999999994 +ejm_43,ejm_44,2.801995613282796,0.049524490706184865,1.541507955047143,0.04723587312934356,1.2604876582356528,0.06843904506930551,0.8399999999999999 +ejm_42,ejm_54,-9.918167499962225,0.055933310929382814,-11.144689365244167,0.05679590871743093,1.2265218652819425,0.0797139292630953,-0.7499999999999996 +ejm_31,ejm_48,22.32769293386505,0.06700551126417102,22.209117478959595,0.06585843168263811,0.11857545490545182,0.09395249631313508,0.5400000000000001 +ejm_31,ejm_49,20.506238300985817,0.07091183298664748,19.28568735282859,0.06848553421033553,1.2205509481572272,0.09858375349722298,1.7899999999999994 +ejm_44,ejm_42,-4.387902534164633,0.058663310907142684,-2.340664805849037,0.05699933643473747,-2.047237728315596,0.08179430542885292,-2.359999999999999 +ejm_45,ejm_42,4.077782935762041,0.05906390933507306,4.325483287631461,0.05833021056414651,-0.24770035186941936,0.08301179946489173,-0.21999999999999945 +ejm_45,ejm_54,-3.546204908950753,0.059109225691869396,-4.372913927450375,0.06047293374488686,0.8267090184996221,0.08456285400579755,-0.969999999999999 +ejm_46,ejm_48,36.82718307494925,0.06215029248223672,35.785088930766065,0.0607516589037281,1.0420941441831797,0.08691043041650695,2.310000000000001 +ejm_46,jmc_27,-2.6477585425837376,0.05159753561569482,-1.9664929406352463,0.05101816587598408,-0.6812656019484913,0.07256141489085176,0.030000000000000387 +ejm_46,ejm_49,34.02088572829551,0.07122752545182358,31.61580792733452,0.06906819876200293,2.4050778009609908,0.09921580752187485,3.56 +ejm_47,ejm_42,-15.094107763737814,0.06185406546332601,-15.324080617083949,0.06286003657019981,0.22997285334613488,0.0881890560781114,-0.07999999999999934 +ejm_48,ejm_47,-6.80735619949554,0.06085408053962775,-6.224032298319523,0.06121851751752865,-0.5833239011760165,0.08631874654654957,-0.7000000000000006 +ejm_50,ejm_45,-4.344320983118319,0.04912769263576972,-5.026217070476791,0.04600616431209978,0.681896087358472,0.06730599778939902,-0.5799999999999991 +ejm_50,ejm_44,9.56939393539365,0.06133730546217391,7.476808306577861,0.0605373642664224,2.0925856288157894,0.08618026174064189,1.5600000000000007 +ejm_50,ejm_55,1.749506539302591,0.04977762939423038,1.6181435061562208,0.04979721631030706,0.1313630331463703,0.07041004999547194,-0.2299999999999996 +ejm_49,jmc_23,-36.94183997988145,0.0716456805797598,-33.8650462386859,0.0709400425398558,-3.0767937411955533,0.10082456635807327,-3.9499999999999984 +jmc_27,jmc_23,-0.21114049009308597,0.04067715991751374,-0.4808335387918212,0.04105345919898118,0.2696930486987353,0.0577928875481871,-0.41999999999999865 +ejm_55,ejm_43,6.199237824609082,0.048971859928771476,5.12918494703228,0.05042264969363981,1.0700528775768023,0.07029001826013938,0.9500000000000004 +jmc_28,jmc_23,-12.346410135979445,0.03244927667360098,-12.033836763691394,0.03333618570175521,-0.3125733722880517,0.04652157385323301,-0.7199999999999974 +ejm_55,ejm_47,19.840091390687206,0.06405191670485884,19.38389100964774,0.06339032062560136,0.45620038103946603,0.09011648452188264,-0.48999999999999955 +jmc_30,jmc_27,3.6602292952564595,0.040114308861549715,3.450340201937055,0.04028962108484178,0.20988909331940453,0.05685429924464757,-0.340000000000001 +jmc_30,ejm_46,6.097156619577483,0.046700150539325094,5.50463365559905,0.04668729013347382,0.5925229639784328,0.0660348932035389,-0.3700000000000014 +jmc_28,ejm_54,-3.0696179557890613,0.05940092363535284,-4.0289091143644775,0.0574875350271607,0.9592911585754165,0.08266369464421516,0.45000000000000245 +jmc_30,jmc_28,15.450604297381329,0.05241798426654849,14.704199201990624,0.05193968512568908,0.7464050953907047,0.07379279074221175,-0.040000000000002214 diff --git a/summaries/dec_08_2025/jacs/tyk2/dg_plot.png b/summaries/dec_08_2025/jacs/tyk2/dg_plot.png new file mode 100644 index 0000000..d0b60bb Binary files /dev/null and b/summaries/dec_08_2025/jacs/tyk2/dg_plot.png differ diff --git a/summaries/dec_08_2025/jacs/tyk2/dg_results.csv b/summaries/dec_08_2025/jacs/tyk2/dg_results.csv new file mode 100644 index 0000000..f25846b --- /dev/null +++ b/summaries/dec_08_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,-9.580108400626022,0.049973871248524114,-9.54 +ejm_50,O=C(CO)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.172798218367937,0.04085317260871646,-8.98 +ejm_43,CC(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.300947318119047,0.051807254818875555,-8.26 +ejm_42,CCC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.877179650280933,0.04149537361883334,-9.78 +ejm_44,CC(C)(C)C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-7.987981620118471,0.05463477357677725,-7.42 +ejm_54,CCNC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-8.880777582941244,0.04823674483986049,-10.53 +ejm_48,O=C(Nc1ccnc(NC(=O)C2CCCC2)c1)c1c(Cl)cccc1Cl,-9.372845140365659,0.053146041589917814,-9.0 +ejm_49,O=C(Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1)c1ccccc1,-7.946266777949993,0.057297566992496274,-7.75 +ejm_45,O=C(CC1CC1)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-9.590560372962905,0.04651275477900627,-9.56 +ejm_46,O=C(Nc1ccnc(NC(=O)C2CC2)c1)c1c(Cl)cccc1Cl,-10.33909526906092,0.05305755112826693,-11.31 +jmc_27,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2Cl)c1)c1c(Cl)cccc1Cl,-10.876559677763955,0.05614732246123645,-11.28 +ejm_47,O=C(Nc1ccnc(NC(=O)C2CCC2)c1)c1c(Cl)cccc1Cl,-9.956122559154304,0.0568979677442863,-9.7 +ejm_55,COC(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.254568480145789,0.04758968463268204,-9.21 +jmc_23,O=C(Nc1ccnc(NC(=O)[C@H]2C[C@H]2F)c1)c1c(Cl)cccc1Cl,-10.603417858188342,0.05303937165196278,-11.7 +jmc_28,C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-10.199267751565754,0.05306590341445475,-10.98 +jmc_30,N#C[C@@H]1C[C@@H]1C(=O)Nc1cc(NC(=O)c2c(Cl)cccc2Cl)ccn1,-11.00150332238872,0.04973192334979701,-10.94 diff --git a/summaries/dec_08_2025/malt1/README.md b/summaries/dec_08_2025/malt1/README.md new file mode 100644 index 0000000..e31d5cf --- /dev/null +++ b/summaries/dec_08_2025/malt1/README.md @@ -0,0 +1,38 @@ +# Malt1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.22 +- RMSE: 1.99 +- R²: 0.37 +- Kendall 𝜏: 0.53 +- Spearman ρ: 0.65 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.10 Hours +- Total Nanoseconds Simulated: 2848.20 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/malt1/ddg_results.csv b/summaries/dec_08_2025/malt1/ddg_results.csv new file mode 100644 index 0000000..5321d99 --- /dev/null +++ b/summaries/dec_08_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) +Pfizer-01-02,Pfizer-01-08,-9.013447302612448,0.061516645067151265,-8.106701977193124,0.06054640571623438,-0.9067453254193245,0.08631433754291767,2.1342033016841935 +1832576-04-1,1832577-09-9,1.4672644690287533,0.05983370649712991,0.020720048260739934,0.05955770913932421,1.4465444207680134,0.08442270518710608,1.645852349536163 +2714550-01-1,1832577-09-9,0.5530032173685736,0.06010319047492696,-0.814091270608367,0.06208055809274906,1.3670944879769404,0.08640827042808195,0.38622292552512305 +1832576-04-1,Pfizer-01-02,-0.18670207397515937,0.06328195370146761,-1.7326897995743715,0.0631016105117524,1.5459877255992123,0.08936676626941133,1.4466222234101842 +1832576-04-1,Pfizer-01-01,3.2631158759263053,0.06894145997518508,1.755979698083695,0.07001403635756098,1.5071361778426102,0.09825930078413911,1.1857247500970411 +Pfizer-01-01,1832577-09-9,-1.9162246715099112,0.0740349162403542,-1.6081470773773003,0.08485814396833376,-0.3080775941326108,0.11261471227360446,0.46012759943912185 +Pfizer-01-03,Pfizer-01-05,13.737812937760427,0.05518680999278112,11.504314110266407,0.05586727781944639,2.23349882749402,0.07852857268621742,1.652050803490815 +Pfizer-01-04,Pfizer-01-11,5.290672808522236,0.03802281104286303,-1.0631341472653435,0.041104211848601246,6.353806955787579,0.05599366384954603,0.7368826744125285 +Pfizer-01-03,Pfizer-01-11,17.09694283409428,0.061752458494207296,8.461082549355163,0.06152571126693457,8.635860284739115,0.08717097726296863,1.8731752673036195 +Pfizer-01-04,Pfizer-01-08,-1.6082469486275757,0.054472559301844546,-0.702569299151298,0.05472140642056357,-0.9056776494762777,0.07721199413004087,0.7368826744125285 +Pfizer-01-04,Pfizer-01-10,3.679000026359828,0.06098293871704444,5.11834836043029,0.06183616073064305,-1.4393483340704623,0.0868483136766208,0.7368826744125285 +Pfizer-01-04,Pfizer-01-12,14.974421702635302,0.05049738406532044,15.24475974212625,0.05291825867984968,-0.27033803949094776,0.07314593562972563,0.7368826744125285 +Pfizer-01-05,Pfizer-01-08,-0.47180299504770784,0.05088191980706148,2.472999903917842,0.0541192671564252,-2.94480289896555,0.07428233195586122,0.22112446381280448 +Pfizer-01-04,Pfizer-01-13,3.4235539724838597,0.05605880979373553,2.509395877043974,0.057497299702341804,0.9141580954398857,0.08030273736648791,0.7368826744125285 +Pfizer-01-05,Pfizer-01-13,3.628225002831693,0.0476579472384567,3.6144282065542805,0.048838535765859385,0.013796796277412243,0.06823842400536995,0.22112446381280448 +Pfizer-01-06,Pfizer-01-03,-17.130482554694133,0.051347926297106695,-15.357455780589577,0.050404866515088034,-1.7730267741045556,0.0719531799395756,-1.6856811149845812 +Pfizer-01-06,Pfizer-01-04,-6.496178094444709,0.0662791575242085,-6.1405577887305265,0.06600376806041977,-0.3556203057141825,0.09353835641218278,-0.5493885220934902 +Pfizer-01-06,Pfizer-01-11,-0.9506913638537505,0.06866936894479658,-7.02563938519567,0.06697966600578997,6.074948021341919,0.09592579366116169,0.18749415231903838 +Pfizer-01-09,2714550-01-1,-8.060710598101778,0.04668760418785755,-3.5463916443028802,0.04755803164788766,-4.514318953798898,0.06664457036416048,-2.3211961010833377 +Pfizer-01-07,2714550-01-1,-10.376046285319783,0.06712611684735706,-10.156932570460476,0.06982525542700015,-0.21911371485930645,0.09685805004464444,-2.3080896267484032 +Pfizer-01-07,Pfizer-01-01,-9.691921894912808,0.06724272759655857,-9.80720689246098,0.06765042352630703,0.11528499754817235,0.0953842975437451,-2.381994300662402 +Pfizer-01-07,Pfizer-01-12,-1.7454569501366903,0.06804737591586243,-5.321690150145777,0.0687375049646842,3.5762332000090864,0.0967227478817919,0.013106474334934547 +Pfizer-01-09,Pfizer-01-02,-8.537651701771223,0.0442308285736192,-5.921587611589673,0.04531507926962657,-2.61606409018155,0.06332316010372058,-2.1342033016841935 +Pfizer-01-09,Pfizer-01-10,-8.89667060519189,0.03885075384319065,-7.799991969440827,0.04258359384550354,-1.0966786357510638,0.05764324365424797,0.0 +Pfizer-01-10,Pfizer-01-02,0.6818833002029437,0.03506668001772705,1.790745189370774,0.04109721538743554,-1.1088618891678304,0.05402456071146647,-2.1342033016841935 +Pfizer-01-13,Pfizer-01-12,12.50161040312141,0.05705918385477323,13.440515012369946,0.05764109344506951,-0.9389046092485371,0.08110638763818821,0.0 diff --git a/summaries/dec_08_2025/malt1/dg_plot.png b/summaries/dec_08_2025/malt1/dg_plot.png new file mode 100644 index 0000000..4510c8c Binary files /dev/null and b/summaries/dec_08_2025/malt1/dg_plot.png differ diff --git a/summaries/dec_08_2025/malt1/dg_results.csv b/summaries/dec_08_2025/malt1/dg_results.csv new file mode 100644 index 0000000..4fdd909 --- /dev/null +++ b/summaries/dec_08_2025/malt1/dg_results.csv @@ -0,0 +1,17 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +Pfizer-01-02,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-8.42986043318091,0.048276361527548724,-8.584573845890262 +Pfizer-01-08,CCOc1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(C)nn12,-8.44035486350629,0.051147301955236604,-6.450370544206068 +1832576-04-1,CO[C@@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.417678447424699,0.06925217317520845,-10.031196069300446 +1832577-09-9,CO[C@H](C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-9.133237229108147,0.06647761459639061,-8.385343719764283 +2714550-01-1,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2cc(Cl)nn12,-10.434700585005977,0.05591615397608182,-8.771566645289406 +Pfizer-01-01,CC(C)c1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)cnc2ccnn12,-9.22508293419779,0.07023224763798189,-8.845471319203405 +Pfizer-01-03,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)n2n1,-8.20244545553083,0.05937066179437075,-8.323545811509687 +Pfizer-01-05,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)cn2n1,-5.71533614312218,0.0544236931320413,-6.671495008018873 +Pfizer-01-04,Cc1cc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,-6.580026380792801,0.037275668210442606,-7.187253218618596 +Pfizer-01-11,Cc1cc2nnc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C)n2n1,-0.07056196265241996,0.0508381555051708,-6.450370544206068 +Pfizer-01-10,Cc1nc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C(C)C)n2n1,-7.360887933324253,0.04469822266831179,-6.450370544206068 +Pfizer-01-12,Cc1c(NC(=O)Nc2ccnc(C(F)(F)F)c2)ccc2cncn12,-6.656145311802571,0.05046960782013296,-6.450370544206068 +Pfizer-01-13,O=C(Nc1ccnc(C(F)(F)F)c1)Nc1cnc2ccnn2c1,-5.6955130371296185,0.05607976332814025,-6.450370544206068 +Pfizer-01-06,Cc1nc2c(C3CC3)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1C,-6.298962953796967,0.06087018279128938,-6.6378646965251065 +Pfizer-01-09,Cc1cn2c(C(C)C)c(NC(=O)Nc3ccnc(C(F)(F)F)c3)cnc2n1,-6.019539195933532,0.0500525118988708,-6.450370544206068 +Pfizer-01-07,Cn1ncc2ncc(NC(=O)Nc3ccnc(C(F)(F)F)c3)c(C3CC3)c21,-9.923677751388494,0.05905234470878661,-6.463477018541003 diff --git a/summaries/dec_08_2025/merck/cdk8/README.md b/summaries/dec_08_2025/merck/cdk8/README.md new file mode 100644 index 0000000..6938a8a --- /dev/null +++ b/summaries/dec_08_2025/merck/cdk8/README.md @@ -0,0 +1,38 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.41 +- RMSE: 1.66 +- R²: 0.63 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.86 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 20.15 Hours +- Total Nanoseconds Simulated: 8039.00 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/cdk8/ddg_results.csv b/summaries/dec_08_2025/merck/cdk8/ddg_results.csv new file mode 100644 index 0000000..b7fe5a3 --- /dev/null +++ b/summaries/dec_08_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) +16,13,20.853144754104154,0.07215742690201903,22.76749917791894,0.07187002787943236,-1.9143544238147834,0.10184299271187293,-1.9935981948721846 +16,14,-7.629537223260314,0.07172899125819392,-10.821133813273727,0.06873553297756015,3.1915965900134133,0.09934596962447603,0.9524348831554853 +16,15,6.6024673689648194,0.05808165208609487,5.302158128657037,0.05744554773742068,1.3003092403077818,0.08169130470192312,1.6026384746345999 +17,14,-2.934222654413268,0.07741402116531956,-5.7773860550877325,0.07308104601498683,2.843163400674464,0.10646018015966893,0.654953933440404 +17,15,1.3341503570944857,0.0631837766571972,2.187239347874431,0.06012761721375391,-0.8530889907799455,0.08722109827599221,1.3051575249195184 +17,16,-2.1670354113662373,0.06632602306545836,-0.6475986151381732,0.0642172338175931,-1.5194367962280642,0.0923200652884471,-0.2974809497150813 +18,14,-0.883822565403385,0.07400804109423054,-5.303695430393834,0.07217445420869585,4.419872864990448,0.10337476474908394,2.641496841687833 +18,15,3.8458870769814304,0.05994576879840077,2.7936505354115955,0.058747434832118764,1.0522365415698351,0.08393304650842456,3.2917004331669477 +18,19,3.05405675836758,0.07586296918112284,3.568714814966721,0.07345075689088576,-0.5146580565991409,0.10559452533545476,0.24172400961419577 +18,45,62.10274496788767,0.07502556649092407,63.696414029579564,0.07372434506930071,-1.5936690616918907,0.10518609548405812,-0.21263703301145156 +19,25,-28.37316399123795,0.06995542037497803,-28.15821970055481,0.06998942804902605,-0.21494429068313636,0.09895595423454663,0.9433766277429518 +19,27,2.286029370544243,0.07035177275066401,-1.2661214303015802,0.06658296243388358,3.552150800845823,0.09686414618233634,2.2737977965705753 +19,36,61.11340048998855,0.07063873024460195,63.4234957737959,0.06861107949346969,-2.3100952838073523,0.09847492289831386,-0.5462602459540326 +19,39,24.223025609856368,0.0703996791232429,28.34592421369925,0.07094074090160707,-4.12289860384288,0.09994350174135638,-0.7879842555682249 +20,19,-5.830438758445363,0.05931270605745873,-6.794577944398287,0.057402776875652824,0.9641391859529235,0.0825413586809333,-0.03847559208419652 +20,23,-0.06711536763024079,0.07615529817343811,-1.7359097613090926,0.07405718486699756,1.6687943936788516,0.10622662599513323,1.6846621986228247 +20,32,-13.134392070082006,0.06752882485902423,-14.554446020688763,0.06693020237336106,1.420053950606757,0.09507783220383095,1.149341062553089 +21,26,9.858667515685106,0.0673520964080956,11.099854429730817,0.06662869644941373,-1.2411869140457108,0.09474010809110112,-0.46094856558431496 +21,32,-26.027140364319408,0.06703369839564711,-23.873684872885168,0.06273507526288188,-2.1534554914342405,0.09181070955415843,0.2049444777403876 +22,21,0.9223245733349793,0.05989184022147668,-3.674027983525126,0.05816915390893606,4.596352556860105,0.08349061618886511,0.5311666609864916 +22,34,41.783114371198685,0.07798744528818082,43.92199397211612,0.07839344188296433,-2.138879600917434,0.11057835842892,-0.9060665585360537 +22,36,42.39726973611764,0.08114444170647026,42.5670127200405,0.08131018252619872,-0.1697429839228581,0.11487282621359371,-0.997965761864439 +24,23,3.314492159145425,0.07254413861383975,3.412736561266285,0.07100696780746332,-0.09824440212086033,0.10151178022492822,1.3301187773619203 +24,26,18.979524522938725,0.062416685221621894,18.207607487522015,0.061389471080476946,0.77191703541671,0.0875471858690829,0.1289045979674821 +24,32,-10.81589098823631,0.06240996417169868,-9.659024970373341,0.060382839462672144,-1.1568660178629702,0.08683945491242762,0.7947976412921847 +27,23,4.315902062332202,0.07746029540830889,6.108817872845175,0.07499350888130914,-1.7929158105129728,0.10781522962491649,-0.550660005863554 +28,19,-39.01166248803592,0.06806198570212997,-36.97652271933571,0.06580353750110295,-2.035139768700199,0.09467068947343737,-4.531390204645579 +28,23,-32.18981244896087,0.06460073673198759,-30.997346090967433,0.06580243759597403,-1.1924663579934374,0.0922128840232623,-2.8082524139385576 +28,26,-15.944423685619403,0.06636636378893633,-14.405141318238835,0.06622465821211909,-1.539282367380568,0.09375606432587405,-4.009466593332996 +29,32,25.33276341697441,0.07125511563202375,22.985182455408182,0.07091296375388248,2.3475809615662273,0.10052830413417171,-0.2935971264555416 +29,34,85.76522213952124,0.08224411848812029,88.9721869132514,0.0823430694255526,-3.206964773730159,0.11638073770306384,-1.9357748237184744 +29,37,53.54855028337688,0.07985631016299677,56.77639048785781,0.07993925211080309,-3.2278402044809287,0.11299254090816473,-2.269398036661052 +30,31,-0.4939436741150915,0.05059066435148892,0.1436594369268568,0.05034001118800195,-0.6376031110419483,0.0713689851821726,-0.24172400961419235 +30,42,-3.0879589959151432,0.071928504015168,-4.109785355280778,0.07282079473502345,1.021826359365634,0.10235515539385624,0.1715059142120209 +30,38,5.187120694841863,0.041295376122768485,4.305240563824747,0.04049197091217995,0.8818801310171165,0.0578351778546046,0.30453623633984195 +31,37,5.290288314358654,0.042660296460867345,4.937833233284148,0.04328038228671647,0.35245508107450635,0.06077081853170494,0.41322992382621326 +32,25,-20.91394580358298,0.07289118553646917,-20.35919076607214,0.07461418769377733,-0.5547550375108434,0.10430916514915746,-0.2444400268943337 +33,23,16.933611182612655,0.06760286051204671,17.69458507275585,0.0656875432550878,-0.7609738901431954,0.09426027842256926,2.097892122449038 +33,27,14.52878241467817,0.07339179721886414,11.933797423126265,0.0702491219981927,2.5949849915519057,0.10159377461504143,2.648552128312592 +33,32,11.321686631133387,0.060283691801950375,10.39489340285539,0.05806517939451784,0.926793228277997,0.08369999137031066,1.5625709863793023 +34,36,1.0269423776687754,0.04648432812454215,-0.19849422188387347,0.046470631217820496,1.2254365995526488,0.06572908280945942,-0.09189920332838528 +35,19,-53.79971098317298,0.0703641897272146,-56.95390995285871,0.07139543254251694,3.154198969685733,0.10024184248057565,0.7879842555682249 +35,25,-85.93533232048216,0.08022527656422891,-88.64979873954051,0.0802528924646895,2.7144664190583465,0.11347520323293558,1.7313608833111769 +35,32,-63.109945237103126,0.07640009682305224,-66.42167490565049,0.07350312401393445,3.3117296685473696,0.1060173760964663,1.9758009102055105 +38,31,-5.127910583370809,0.05167344672719943,-4.195544946776894,0.05086477964811836,-0.932365636593915,0.07250772996943397,-0.5462602459540343 +38,40,-0.6243549699626784,0.06681432667311316,0.6132650082739673,0.06734845214842762,-1.2376199782366457,0.09486816249707025,0.20059289081475665 +38,41,0.6731068587186645,0.07135727898862881,1.4990728301313792,0.07223036637809627,-0.8259659714127147,0.10153367466892463,0.10869368748637136 +40,39,-1.9227747660533314,0.03734659432214659,-1.8791346831226068,0.0360279122344898,-0.043640082930724515,0.05189198943419968,-0.33362321294257763 +41,39,-3.3337115445007486,0.03759007693305477,-2.907682060914123,0.038054135928802316,-0.42602948358662557,0.05348954239027232,-0.24172400961419235 +41,40,-3.086656522755195,0.039165002184013996,-2.18383095753418,0.03791723659749487,-0.9028255652210152,0.05451251440966767,0.09189920332838528 +42,13,-2.8799622762079267,0.06519112963189741,-3.7989057985759773,0.06610628891554288,0.9189435223680504,0.0928435502168464,0.24172400961419235 +42,18,-20.311814848410823,0.06894436145547257,-24.39884645976458,0.06958710320402625,4.087031611353759,0.0979575924001333,0.5462602459540292 +43,13,-7.640736708887137,0.06921469608467593,-8.473429615745102,0.06838388805137974,0.8326929068579659,0.09729866545393975,0.6549539334404056 +43,37,3.201251110250436,0.07592024740002905,,,,,0.41322992382621326 +43,44,29.26852749363631,0.06987383786790714,30.416922422966916,0.06859630104004846,-1.1483949293306084,0.09791734133833255,0.41322992382621326 +43,45,35.229229153690326,0.07207937899819927,34.43194100866208,0.07258911780399126,0.7972881450282425,0.1022967101148799,0.746853136768791 +44,18,-52.83237885786077,0.0633952559790062,-56.71578844070094,0.06533724346358648,3.8834095828401716,0.09103798033822859,0.5462602459540292 +44,45,5.7978796445924345,0.05632342776823039,3.828741587536548,0.055541798621420876,1.9691380570558867,0.07910259104268037,0.33362321294257763 diff --git a/summaries/dec_08_2025/merck/cdk8/dg_plot.png b/summaries/dec_08_2025/merck/cdk8/dg_plot.png new file mode 100644 index 0000000..bb88bae Binary files /dev/null and b/summaries/dec_08_2025/merck/cdk8/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/cdk8/dg_results.csv b/summaries/dec_08_2025/merck/cdk8/dg_results.csv new file mode 100644 index 0000000..a40f3f3 --- /dev/null +++ b/summaries/dec_08_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,-8.81095435206714,0.0804412493996691,-9.292698790319301 +13,Cc1cccc(Cc2n[nH]c3cc(O)c(C(=O)N4CC[C@H](O)C4)cc23)c1,-11.060071076826729,0.08196010254116232,-11.286296985191486 +14,CNC(=O)c1ccc2[nH]nc(CC(C)C)c2c1,-4.871907140117613,0.07935634700503469,-8.340263907163816 +15,CNC(=O)c1ccc2[nH]nc(Cc3ccc(OC)c(OC)c3)c2c1,-7.814609261692204,0.08055109208877148,-7.690060315684702 +17,CNC(=O)c1ccc2[nH]nc(Cc3ccc4cnn(C)c4c3)c2c1,-7.2736935021622875,0.0854683760718953,-8.995217840604221 +18,CNC(=O)c1ccc2[nH]nc(Cc3ccc4c(cnn4C)c3)c2c1,-8.89864106614316,0.062002600873266374,-10.981760748851649 +19,CNC(=O)c1ccc2[nH]nc(Cc3ccc(-c4cnn(C)c4)cc3)c2c1,-9.44769165059492,0.04383023950370516,-10.740036739237453 +45,COC1CN(C(=O)c2ccc3[nH]nc(Cc4ccc5c(cnn5C)c4)c3c2)C1,-10.745483880906642,0.08634001274298103,-11.1943977818631 +25,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(NS(C)(=O)=O)cc34)cc2)cn1,-9.534548904310483,0.07431560634908888,-9.796660111494502 +27,CC(=O)NCCNc1ccc2[nH]nc(Cc3ccc(-c4cnn(C)c4)cc3)c2c1,-6.326831025774603,0.07670999205077707,-8.466238942666878 +36,COC1CN(C(=O)c2ccc3[nH]nc(Cc4ccc(-c5cnn(C)c5)cc4)c3c2)C1,-11.955950057365438,0.07467186742861077,-11.286296985191486 +39,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCOCC5)cc34)cc2)cn1,-13.787780559074907,0.07010752381884143,-11.52802099480568 +20,CNC(=O)c1ccc2[nH]nc(Cc3ccc(-c4cnn(CC(C)(C)O)c4)cc3)c2c1,-10.321840767359564,0.0663852747271492,-10.701561147153257 +23,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(-c5cc(N)ccn5)cc34)cc2)cn1,-8.665358229143672,0.05843565271548393,-9.016898948530432 +32,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(N)=O)cc34)cc2)cn1,-8.772522142507324,0.05558053580637544,-9.552220084600169 +21,Cn1cnc(-c2ccc3[nH]nc(Cc4ccc(-c5cnn(C)c5)cc4)c3c2)c1,-6.75754084985481,0.07490170038962063,-9.757164562340556 +26,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(N5CCCC5=O)cc34)cc2)cn1,-8.04368952480572,0.07882714047199152,-10.218113127924871 +22,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(-c5nccn5C)cc34)cc2)cn1,-11.433488998191741,0.08324564149801794,-10.288331223327047 +34,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CC(F)(F)C5)cc34)cc2)cn1,-13.385152003195751,0.08349150126454455,-11.1943977818631 +24,CC(=O)Nc1ccc2[nH]nc(Cc3ccc(-c4cnn(C)c4)cc3)c2c1,-8.306789361593664,0.06912213772239044,-10.347017725892353 +28,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(N5CCOCC5)cc34)cc2)cn1,-7.131987161326146,0.06627769212412471,-6.208646534591875 +29,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(S(=O)(=O)NC5CC5)cc34)cc2)cn1,-10.609625886010233,0.07000374676242808,-9.258622958144626 +37,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCCC5)cc34)cc2)cn1,-13.599239305627641,0.08044087365911326,-11.52802099480568 +30,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CC[C@H](O)C5)cc34)cc2)cn1,-13.430887059833061,0.06617743639098483,-11.699526909017699 +31,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CC[C@@H](O)C5)cc34)cc2)cn1,-13.8827845509353,0.07480342664154997,-11.941250918631892 +42,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CC[C@H](O)C5)cc34)ccc21,-12.441375454712247,0.07304484767554535,-11.52802099480568 +38,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCC(F)(F)C5)cc34)cc2)cn1,-12.660641985437048,0.06285768028096027,-11.394990672677858 +33,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)NC5CC5)cc34)cc2)cn1,-8.911792621784636,0.06966430755265283,-11.11479107097947 +35,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CC(O)C5)cc34)cc2)cn1,-12.32588356469235,0.07655224629602955,-11.52802099480568 +40,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCNCC5)cc34)cc2)cn1,-13.925344726331254,0.06661998673679029,-11.1943977818631 +41,Cn1cc(-c2ccc(Cc3n[nH]c4ccc(C(=O)N5CCCCC5)cc34)cc2)cn1,-13.231429204353272,0.06729163421339196,-11.286296985191486 +43,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CCC(F)(F)C5)cc34)ccc21,-11.690519578330923,0.09251517653867039,-11.941250918631892 +44,Cn1ncc2cc(Cc3n[nH]c4ccc(C(=O)N5CC(O)C5)cc34)ccc21,-12.769458020596167,0.08996258761256011,-11.52802099480568 diff --git a/summaries/dec_08_2025/merck/cmet_neutral/README.md b/summaries/dec_08_2025/merck/cmet_neutral/README.md new file mode 100644 index 0000000..e649384 --- /dev/null +++ b/summaries/dec_08_2025/merck/cmet_neutral/README.md @@ -0,0 +1,38 @@ +# Cmet Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.23 +- RMSE: 1.42 +- R²: 0.72 +- Kendall 𝜏: 0.56 +- Spearman ρ: 0.70 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 5.62 Hours +- Total Nanoseconds Simulated: 2379.80 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/cmet_neutral/ddg_results.csv b/summaries/dec_08_2025/merck/cmet_neutral/ddg_results.csv new file mode 100644 index 0000000..9c7cdc8 --- /dev/null +++ b/summaries/dec_08_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_200,2.6396006294721572,0.048733320134872866,3.5435649942466165,0.047562075084381567,-0.9039643647744594,0.06809616345801249,-0.24172400961419577 +CHEMBL3402747_3400,CHEMBL3402749_500,45.52173318265448,0.05573876228761368,46.25283727624747,0.0524730813313935,-0.7311040935929861,0.07655216447473018,-1.1428017125783134 +CHEMBL3402744_300,CHEMBL3402747_3400,-37.385148850402565,0.056971532470068,-37.24792402845906,0.056952788179627234,-0.13722482194350194,0.08055666076384684,1.447337948918152 +CHEMBL3402744_300,CHEMBL3402752_30000,6.529980317128078,0.06104864490805594,5.244231094279044,0.06226994550985132,1.285749222849033,0.0872036877598061,2.74544018721291 +CHEMBL3402745_200,CHEMBL3402751_2100,9.460755039926337,0.07074540836753553,7.377026540255498,0.07220569475092599,2.0837284996708387,0.1010869682973689,1.4018070702091983 +CHEMBL3402745_200,CHEMBL3402754_40,-30.108210169965744,0.0739823081707071,-24.70445185462813,0.08054766467458553,-5.403758315337616,0.10936776584896916,-0.9594901697802458 +CHEMBL3402747_3400,CHEMBL3402755_4200,64.49972518782472,0.06542197422089972,65.74579706730289,0.06838170699273287,-1.2460718794781644,0.09463663435583515,0.1259750355030604 +CHEMBL3402748_5300,CHEMBL3402751_2100,-0.7516415536769832,0.06601021281264778,-1.4936283294415351,0.06449308118763414,0.7419867757645519,0.09228599957006381,-0.5519111390863394 +CHEMBL3402750_400,CHEMBL3402748_5300,4.047715693948747,0.05497223688422817,0.9633997780343634,0.05513424004774606,3.084315915914383,0.07785712076424468,1.540488285469326 +CHEMBL3402750_400,CHEMBL3402754_40,-13.357950293327171,0.055577039716195716,-12.831195654856906,0.055993442971213975,-0.5267546384702662,0.07889279434388281,-1.3727200936064574 +CHEMBL3402749_500,CHEMBL3402761_1,12.215000923200268,0.08322880073432203,18.004345922691876,0.08231134993722851,-5.789344999491608,0.11705636078471929,-3.7049303569931555 +CHEMBL3402752_30000,CHEMBL3402751_2100,6.285845234824249,0.05554595164973787,6.416969007995889,0.05514702803859194,-0.1311237731716402,0.07827226485904355,-1.5853571266179074 +CHEMBL3402753_200,CHEMBL3402754_40,-23.63324351453766,0.03605476998464594,-22.646347616356497,0.03833315022166135,-0.9868958981811647,0.05262486906931153,-0.9594901697802458 +CHEMBL3402752_30000,CHEMBL3402749_500,1.895834743661269,0.06236662883301739,4.3916033930251315,0.06069538914881441,-2.4957686493638627,0.08702601137545816,-2.4409039508730714 +CHEMBL3402753_200,CHEMBL3402750_400,-10.188464006571891,0.05772103873658509,-9.640782523279126,0.05805458589304208,-0.5476814832927659,0.08186606901545326,0.4132299238262116 +CHEMBL3402755_4200,CHEMBL3402754_40,-29.340109230495244,0.04028921600340523,-27.11864268906586,0.042942192584122366,-2.2214665414293844,0.05888338331058176,-2.774527163815654 +CHEMBL3402753_200,CHEMBL3402748_5300,-5.857536209344522,0.07515880769279104,-9.0510353814668,0.07301160527375611,3.1934991721222783,0.10478330438792584,1.9537182092955376 +CHEMBL3402754_40,CHEMBL3402761_1,24.040368774804076,0.07145780105808626,27.16935209993804,0.07168477944704621,-3.1289833251339614,0.10121721660087622,-2.1991799412588757 +CHEMBL3402755_4200,CHEMBL3402761_1,-5.6736357909895485,0.07288956411161114,0.2815929078409457,0.07359135661285665,-5.955228698830494,0.10357884110425888,-4.97370710507453 diff --git a/summaries/dec_08_2025/merck/cmet_neutral/dg_plot.png b/summaries/dec_08_2025/merck/cmet_neutral/dg_plot.png new file mode 100644 index 0000000..e048e8e Binary files /dev/null and b/summaries/dec_08_2025/merck/cmet_neutral/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/cmet_neutral/dg_results.csv b/summaries/dec_08_2025/merck/cmet_neutral/dg_results.csv new file mode 100644 index 0000000..b29a947 --- /dev/null +++ b/summaries/dec_08_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,-6.794333963135106,0.04804236883631888,-8.954086721804785 +CHEMBL3402745_200,CCOC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-7.362086578189717,0.04850250749073299,-9.19581073141898 +CHEMBL3402747_3400,Cc1noc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)n1,-7.299998429500154,0.053618299182316635,-7.506748772886633 +CHEMBL3402749_500,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)o1,-8.179769665854407,0.05805214521882413,-8.649550485464946 +CHEMBL3402752_30000,Cc1nc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)cs1,-5.6281965442016135,0.053884586633494914,-6.208646534591875 +CHEMBL3402751_2100,Cc1csc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)n1,-5.8105428901146,0.050045067360817666,-7.794003661209782 +CHEMBL3402754_40,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-11.275644366827548,0.04043653516541174,-10.155300901199226 +CHEMBL3402755_4200,Cc1ccc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nn1,-8.827354454108884,0.04944986325795287,-7.3807737373835725 +CHEMBL3402748_5300,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)[nH]1,-7.067286984185429,0.05556576983257923,-7.242092522123443 +CHEMBL3402750_400,Cc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)s1,-10.54482377753194,0.047634479082688044,-8.782580807592769 +CHEMBL3402761_1,N#Cc1cccc(-c2ccc(=O)n(Cc3cccc(-c4ncc(OCCN5CCOCC5)cn4)c3)n2)c1,-14.417685600486074,0.06668627089901717,-12.354480842458102 +CHEMBL3402753_200,Cc1ccc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-10.212163195417622,0.04695854245745217,-9.19581073141898 diff --git a/summaries/dec_08_2025/merck/cmet_positive/README.md b/summaries/dec_08_2025/merck/cmet_positive/README.md new file mode 100644 index 0000000..a192d74 --- /dev/null +++ b/summaries/dec_08_2025/merck/cmet_positive/README.md @@ -0,0 +1,38 @@ +# Cmet Positive Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 4.86 +- RMSE: 5.98 +- R²: 0.20 +- Kendall 𝜏: 0.37 +- Spearman ρ: 0.51 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 8.72 Hours +- Total Nanoseconds Simulated: 3718.40 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/cmet_positive/ddg_results.csv b/summaries/dec_08_2025/merck/cmet_positive/ddg_results.csv new file mode 100644 index 0000000..51ab337 --- /dev/null +++ b/summaries/dec_08_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,CHEMBL3402763_90,-6.887831660093336,0.07364154150490745,-7.199565558936377,0.07405314199901211,0.31173389884304187,0.10443631779771277,-0.8892720743780677 +CHEMBL3402743_42,CHEMBL3402742_23,0.4573632225402124,0.07548504305159924,1.2345498523191714,0.07617564731361602,-0.777186629778959,0.107241414426285,-0.3589957553370291 +CHEMBL3402741_400,CHEMBL3402764_90,-11.84184126524469,0.07677268375121632,-14.326125910748749,0.07550829613353344,2.484284645504059,0.10768262513216166,-0.8892720743780677 +CHEMBL3402743_42,CHEMBL3402758_10,-3.328689186288813,0.08160668842151911,-0.7758791430174733,0.08396269461982298,-2.55281004327134,0.1170870858931443,-0.8555468242551639 +CHEMBL3402743_42,CHEMBL3402762_1,6.17398081358881,0.08712853257430846,11.581893366372165,0.08881376472059413,-5.407912552783356,0.12441569833585062,-2.228266917861616 +CHEMBL3402741_400,CHEMBL3402760_1,20.73426790495892,0.10584740099690589,26.66286212105782,0.10938697473606918,-5.928594216098901,0.15221426523065842,-3.571900034865333 +CHEMBL3402756_2.7,CHEMBL3402760_1,-0.3785543845741399,0.06381574079091931,0.2934314396388777,0.06337054174100025,-0.6719858242130177,0.08993483381449958,-0.5921417067147577 +CHEMBL3402757_6.5,CHEMBL3402756_2.7,-3.342755616182914,0.06998036583274059,-2.42387789839366,0.06867498371836725,-0.918877717789254,0.0980484828582381,-0.5237607923099594 +CHEMBL3402743_42,CHEMBL3402765_11-charged-pKa-8.1,-19.428879034318648,0.09420293001024406,6.315197995420618,0.09290820037843418,-25.744077029739266,0.13231071657305093,-0.7987262536101402 +CHEMBL3402758_10,CHEMBL3402757_6.5,9.308415743718983,0.06869601528666171,8.683254548278052,0.07015757571615373,0.6251611954409312,0.09818975479464802,-0.25681759458173514 +CHEMBL3402757_6.5,CHEMBL3402742_23,-6.361642780571995,0.08450672155176454,-7.20229432427063,0.08875761624028188,0.8406515436986353,0.12255325547730103,0.75336866349987 +CHEMBL3402759_5.7,CHEMBL3402756_2.7,-5.560255685063119,0.06221487204116647,-4.920183474371713,0.06038528732584748,-0.6400722106914054,0.08670105667478266,-0.4454628959187488 +CHEMBL3402758_10,CHEMBL3402762_1,8.976053407584567,0.08129939472615531,11.627312674684017,0.07924585403847122,-2.6512592670994515,0.11353192046788381,-1.3727200936064523 +CHEMBL3402759_5.7,CHEMBL3402757_6.5,-3.151756275710518,0.06734409489498823,-2.8506323248303,0.06744685163579392,-0.3011239508802181,0.09531162003032985,0.07829789639121063 +CHEMBL3402762_1,CHEMBL3402760_1,-3.3989789739399465,0.06584958402512715,-5.165538736836712,0.06587594937563386,1.7665597628967664,0.09314401978883753,0.0 +CHEMBL3402759_5.7,CHEMBL3402760_1,20.42601766168971,0.0781432223686841,-29.925693554860526,0.08100385772750349,50.351711216550235,0.1125521575488415,-1.0376046026335066 +CHEMBL3402763_90,CHEMBL3402764_90,-4.4444670164179465,0.07570733688605609,-6.549985235830194,0.07541002561413206,2.1055182194122475,0.10685631858483073,0.0 +CHEMBL3402763_90,CHEMBL3402760_1,19.529133889424507,0.10579699047568487,30.837511314664667,0.111872623049854,-11.30837742524016,0.1539756051514878,-2.6826279604872654 +CHEMBL3402765_11-charged-pKa-8.1,CHEMBL3402742_23,-3.363164303698635,0.08318980145116028,-2.7049400874998795,0.08409019191967136,-0.6582242161987555,0.11828653111225569,0.43973049827311106 +CHEMBL3402765_11-charged-pKa-8.1,CHEMBL3402764_90,-1.2142651241776905,0.08077809831799657,-1.6040703948234072,0.08104714273713004,0.3898052706457165,0.11442788346257503,1.253087296235789 diff --git a/summaries/dec_08_2025/merck/cmet_positive/dg_plot.png b/summaries/dec_08_2025/merck/cmet_positive/dg_plot.png new file mode 100644 index 0000000..01cff59 Binary files /dev/null and b/summaries/dec_08_2025/merck/cmet_positive/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/cmet_positive/dg_results.csv b/summaries/dec_08_2025/merck/cmet_positive/dg_results.csv new file mode 100644 index 0000000..9f437e3 --- /dev/null +++ b/summaries/dec_08_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,-4.808806306108234,0.07815581505734036,-8.782580807592769 +CHEMBL3402763_90,CC[NH+](CC)CCCOC(=O)Nc1cccc(CN2N=C(c3ccc(Cl)cc3)CSC2=O)c1,-3.826343566947533,0.08492567189742332,-9.671852881970837 +CHEMBL3402743_42,C[NH+](C)CCCOC(=O)Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1,-4.204900935858978,0.06021240803833591,-10.126213924596485 +CHEMBL3402742_23,C[NH+](C)CCCOC(=O)Nc1cccc(CN2N=C(c3cc(F)cc(F)c3)CSC2=O)c1,-11.367528845010233,0.07132744043976598,-10.485209679933515 +CHEMBL3402764_90,C[NH+](C)CCCOC(=O)Nc1cccc(Cn2nc(-c3ccc(F)cc3)ccc2=O)c1,-5.66057888160526,0.07580666519475049,-9.671852881970837 +CHEMBL3402758_10,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccnc4)ccc3=O)c2)nc1,-11.17937637553677,0.0667927273669494,-10.981760748851649 +CHEMBL3402762_1,C[N@H+]1CC[C@H](COc2cnc(-c3cccc(Cn4nc(-c5cccc(C#N)c5)ccc4=O)c3)nc2)CC1,-9.831798443240434,0.07158805730523805,-12.354480842458102 +CHEMBL3402760_1,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(C#N)c4)ccc3=O)c2)nc1,-5.496392584811352,0.050362664144649086,-12.354480842458102 +CHEMBL3402756_2.7,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cc(F)cc(F)c4)ccc3=O)c2)nc1,-16.482176813719313,0.0679577138599215,-11.762339135743344 +CHEMBL3402757_6.5,C[NH+](C)CCCOc1cnc(-c2cccc(Cn3nc(-c4cccc(F)c4)ccc3=O)c2)nc1,-16.654878557797367,0.06613713389016766,-11.238578343433385 +CHEMBL3402765_11-charged-pKa-8.1,O=C(Nc1cccc(Cn2nc(-c3cc(F)cc(F)c3)ccc2=O)c1)OCCC[NH+]1CCOCC1,-14.33532956396538,0.08486852882282443,-10.924940178206626 +CHEMBL3402759_5.7,COc1cccc(-c2ccc(=O)n(Cc3cccc(-c4ncc(OCCC[NH+](C)C)cn4)c3)n2)c1,-25.823055632439377,0.06730659223436346,-11.316876239824595 diff --git a/summaries/dec_08_2025/merck/eg5_neutral/README.md b/summaries/dec_08_2025/merck/eg5_neutral/README.md new file mode 100644 index 0000000..2bc7f3a --- /dev/null +++ b/summaries/dec_08_2025/merck/eg5_neutral/README.md @@ -0,0 +1,38 @@ +# Eg5 Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.99 +- RMSE: 1.17 +- R²: 0.40 +- Kendall 𝜏: 0.31 +- Spearman ρ: 0.46 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.46 Hours +- Total Nanoseconds Simulated: 1833.60 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/eg5_neutral/ddg_results.csv b/summaries/dec_08_2025/merck/eg5_neutral/ddg_results.csv new file mode 100644 index 0000000..f35265f --- /dev/null +++ b/summaries/dec_08_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,CHEMBL1089056,8.978789324336931,0.042223051910351625,7.958415459521562,0.040945632331775186,1.0203738648153702,0.05881607705103394,0.7518419923407236 +CHEMBL1078774,CHEMBL1089056,8.574545838943132,0.047267471062178164,7.167040718295407,0.0467049301928094,1.4075051206477256,0.06644971275279563,1.1650719161669367 +CHEMBL1078691,CHEMBL1084115,-2.268480518648441,0.05593544049012883,-3.2160197766313976,0.05659288161620428,0.9475392579829566,0.07957089764763532,0.7518419923407236 +CHEMBL1078774,CHEMBL1078998,-1.0883456620110532,0.06174830057908723,-3.3616508544301715,0.06100212803952204,2.273305192419118,0.08679926410837564,0.2299183810281406 +CHEMBL1078691,CHEMBL1088740,6.95880825121761,0.06728386987587977,1.8792638634218284,0.06653271081037447,5.0795443877957815,0.0946241023907294,1.4986951291095145 +CHEMBL1078774,CHEMBL1088740,5.588732763213959,0.06834984605678653,0.8863585650153908,0.0685563333375127,4.702374198198568,0.09680739794391012,1.9119250529357277 +CHEMBL1084115,CHEMBL1078998,0.760351616564098,0.05716672178846554,0.6965648846304742,0.05645288251032635,0.06378673193362389,0.08034277829254183,-0.9351535351387962 +CHEMBL1084115,CHEMBL1089056,11.289255772082209,0.05421990354767759,11.098229864231895,0.054205655500289565,0.19102590785031295,0.07666844871872348,0.0 +CHEMBL1089056,CHEMBL1078998,-10.264000499031633,0.05727010597512779,-10.409989050486702,0.05719815227749962,0.145988551455069,0.0809412976320642,-0.9351535351387962 +CHEMBL1089393,CHEMBL1089056,7.967114005574235,0.044779142354415255,10.164959534191663,0.04539033143059068,-2.1978455286174277,0.06376091104568579,-1.0681838572666138 +CHEMBL1085895,CHEMBL1088740,14.903248083167442,0.07581032224310481,10.485377615669401,0.07453268766492008,4.417870467498041,0.1063124004486773,2.1714463472165977 +CHEMBL1085895,CHEMBL1093088,10.50274701394901,0.08157546703773287,9.65756983659757,0.07651109714206801,0.845177177351439,0.11184142706666081,-0.36135680698486067 +CHEMBL1089393,CHEMBL1093088,0.3142960070575871,0.06330703736177784,1.7159279609073783,0.06133712969807304,-1.4016319538497912,0.0881477422236314,-2.854133874699281 +CHEMBL1089393,CHEMBL1085895,-9.499293060605934,0.07424050259956075,-7.094366912975344,0.07272513499078996,-2.404926147630589,0.10392592306861656,-2.4927770677144205 +CHEMBL1093088,CHEMBL1088740,3.5274755266887152,0.06692740192600534,1.532640071239665,0.06535499125058226,1.9948354554490504,0.09354438523999582,2.532803154201458 diff --git a/summaries/dec_08_2025/merck/eg5_neutral/dg_plot.png b/summaries/dec_08_2025/merck/eg5_neutral/dg_plot.png new file mode 100644 index 0000000..6fe61bf Binary files /dev/null and b/summaries/dec_08_2025/merck/eg5_neutral/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/eg5_neutral/dg_results.csv b/summaries/dec_08_2025/merck/eg5_neutral/dg_results.csv new file mode 100644 index 0000000..a02d986 --- /dev/null +++ b/summaries/dec_08_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,-11.54377816155915,0.03999910546014986,-10.252188960099543 +CHEMBL1089056,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-10.42430879472998,0.03504509959217592,-9.50034696775882 +CHEMBL1078774,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccc(O)c(F)c1)N2,-11.942928556613325,0.04628489373821615,-10.665418883925756 +CHEMBL1084115,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccsc1)N2,-10.477920813754658,0.04749559231717828,-9.50034696775882 +CHEMBL1078998,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1cccs1)N2,-10.142608746749248,0.05050862592631202,-10.435500502897614 +CHEMBL1088740,Cc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-6.8880401556997235,0.05097751703278849,-8.753493830990028 +CHEMBL1089393,Clc1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1ccccc1)N2,-8.186954685999867,0.04669687829715441,-8.432163110492205 +CHEMBL1085895,O=C(NCCCO)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-10.731581554646883,0.06238791559256142,-10.924940178206626 +CHEMBL1093088,FC(F)(F)c1ccc2c(c1)[C@H]1O[C@@H](Cn3cncn3)CC[C@H]1[C@H](c1ccccc1)N2,-9.412574917568062,0.05775694754344618,-11.286296985191486 diff --git a/summaries/dec_08_2025/merck/eg5_positive/README.md b/summaries/dec_08_2025/merck/eg5_positive/README.md new file mode 100644 index 0000000..d91233a --- /dev/null +++ b/summaries/dec_08_2025/merck/eg5_positive/README.md @@ -0,0 +1,38 @@ +# Eg5 Positive Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 3.31 +- RMSE: 3.93 +- R²: 0.07 +- Kendall 𝜏: 0.12 +- Spearman ρ: 0.21 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 12.35 Hours +- Total Nanoseconds Simulated: 5311.00 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/eg5_positive/ddg_results.csv b/summaries/dec_08_2025/merck/eg5_positive/ddg_results.csv new file mode 100644 index 0000000..aeeef0d --- /dev/null +++ b/summaries/dec_08_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) +CHEMBL1077227,CHEMBL1086410,11.00154622692022,0.05763759203021221,10.24521973986834,0.05509300266446979,0.7563264870518804,0.07973287250330603,-0.133030322127821 +CHEMBL1077204,CHEMBL1084676,11.991985327696604,0.0544528585510233,11.090212513722202,0.05476555217539519,0.9017728139744022,0.07722939537154026,0.33362321294258274 +CHEMBL1082248,CHEMBL1085666,-13.661524857907235,0.06645271812448746,-14.9681625587677,0.06410963800344673,1.3066377008604655,0.09233639277698455,1.1309960839922635 +CHEMBL1082249,CHEMBL1085692,22.398475795356905,0.07356558368795142,22.635182410509334,0.0719235979966906,-0.23670661515242755,0.10288293858623275,-0.10869368748637136 +CHEMBL1077227,CHEMBL1084935,21.945898104581783,0.07818649109256737,21.00970772308788,0.07612319895689108,0.9361903814939017,0.10912318181210874,0.7958805930193142 +CHEMBL1082249,CHEMBL1096002,7.625186100582934,0.056121489864344024,8.347632407875015,0.055452598698918755,-0.7224463072920806,0.07889621237459371,0.09189920332838528 +CHEMBL1077204,CHEMBL1085692,-4.81257672095729,0.09022958393745852,-31.67563254864238,0.08836855702652871,26.863055827685088,0.12629481259528327,-0.2801996016983872 +CHEMBL1083517,CHEMBL1083836,5.087606886999102,0.06119103385330799,3.1644482281076733,0.06041516825898955,1.923158658891429,0.08599032026803193,0.603080816599053 +CHEMBL1083517,CHEMBL1085666,-5.868545636671344,0.06143393354178885,-8.92414887639528,0.06153715438191227,3.0556032397239368,0.08695372079353612,0.9594901697802425 +CHEMBL1082249,CHEMBL1096003,1.1679885812838287,0.07768636226086426,2.8549232444465735,0.07604535846837562,-1.6869346631627449,0.10871093517172034,-0.6549539334404056 +CHEMBL1083517,CHEMBL1096002,1.3962217988062349,0.06554083741211154,-0.44779989604024956,0.06410280620021254,1.8440216948464845,0.09167753885997838,0.33362321294257763 +CHEMBL1084143,CHEMBL1084676,7.421846742196709,0.08276656050630549,5.961986257543282,0.0829972557080432,1.4598604846534267,0.117212832032633,1.160083060595004 +CHEMBL1084431,CHEMBL1083517,-15.88669071984941,0.08849166118806569,-14.483368029748346,0.08606434946034297,-1.403322690101063,0.12344167184486546,-1.6621627449787497 +CHEMBL1084677,CHEMBL1084143,16.22679530063498,0.06521667823973899,15.940086792588517,0.06547189968799866,0.2867085080464635,0.09241095589474768,-0.41322992382621326 +CHEMBL1084431,CHEMBL1085666,-23.647586556903747,0.08895027600012947,-24.622630681075183,0.08512324722929245,0.9750441241714336,0.12311831228277317,-0.7026725751985073 +CHEMBL1084677,CHEMBL1077204,19.655364057489297,0.07843638606960522,17.790143665775915,0.07559705140163069,1.8652203917133818,0.1089365909154539,0.4132299238262082 +CHEMBL1084677,CHEMBL1096002,19.852679947557963,0.0779428389296057,17.657147718519724,0.07643722373595303,2.1955322290382404,0.10916838055438306,0.33362321294257763 +CHEMBL1084677,CHEMBL1096003,9.300555541550967,0.06286708198340978,8.29130661575918,0.06300758287144266,1.0092489257917878,0.08900688454501979,-0.41322992382621326 +CHEMBL1084678,CHEMBL1084143,12.454177755569573,0.07765896030474267,12.943151933155747,0.0771773213655384,-0.4889741775861747,0.10948631443597502,-0.746853136768791 +CHEMBL1086409,CHEMBL1082248,-0.7719425392269773,0.054158784802404145,-1.3092524344962324,0.053808068912553714,0.5373098952692551,0.07634449719116142,-1.7657391069515567 +CHEMBL1084678,CHEMBL1096003,4.773531969107042,0.07217530274233083,5.318270395436742,0.07036011619240738,-0.5447384263296997,0.10079593382947637,-0.746853136768791 +CHEMBL1084678,CHEMBL1084676,20.4961289831639,0.08438086655568473,18.15063700334712,0.08318427405159351,2.345491979816781,0.1184894682669261,0.41322992382621326 +CHEMBL1085692,CHEMBL1096002,-12.526691318830558,0.0735869972799056,-11.864788598415027,0.07235176856948246,-0.6619027204155317,0.10319798730500893,0.20059289081475665 +CHEMBL1086409,CHEMBL1077227,-1.4070859293367488,0.0656611704394411,-3.1604468154461607,0.06429344831509616,1.7533608861094119,0.0918968813383962,-1.4612028706117146 +CHEMBL1086409,CHEMBL1083836,-4.752432791866926,0.06113152213375363,-4.294749489668804,0.058813733715945705,-0.4576833021981216,0.08482993735704264,-0.9911523761404827 +CHEMBL1086409,CHEMBL1096002,-8.05361596221045,0.06358506580965785,-7.918820260602648,0.06329659881467657,-0.13479570160780294,0.08971911733585343,-1.260609979796958 +CHEMBL1086410,CHEMBL1083836,-13.971898365025748,0.06517193629458803,-13.725520193778566,0.063649838330712,-0.24637817124718187,0.09109710862542024,0.603080816599053 +CHEMBL1086410,CHEMBL1084935,11.937410503113759,0.06879834279147506,10.94198009970968,0.06771907933332877,0.9954304034040784,0.0965354115162254,0.9289109151471352 +CHEMBL1086409,CHEMBL1084431,6.482616136718205,0.08843371745204211,7.114426515318419,0.08626718085939648,-0.6318103786002145,0.1235416888172387,0.06792955223921412 +CHEMBL1093087,CHEMBL1082248,-6.445084835951229,0.08171130143890361,-5.659616243797715,0.07949665712435319,-0.785468592153514,0.11400199681052234,-1.100416829359156 +CHEMBL1093087,CHEMBL1083517,-13.935907322814492,0.08055674093778764,-11.76733740721337,0.07897445189261044,-2.1685699156011227,0.11281113669428242,-0.9289109151471352 +CHEMBL1093087,CHEMBL1086409,-5.306444691857854,0.08098326920171,-3.822033582114784,0.07942205705153645,-1.4844111097430694,0.11342906610253892,0.6653222775924005 +CHEMBL1096002,CHEMBL1084935,28.58626206886033,0.07006517896692477,26.554310177299442,0.06812146574315715,2.031951891560888,0.09772237921102479,0.5952877022045576 diff --git a/summaries/dec_08_2025/merck/eg5_positive/dg_plot.png b/summaries/dec_08_2025/merck/eg5_positive/dg_plot.png new file mode 100644 index 0000000..68e23fd Binary files /dev/null and b/summaries/dec_08_2025/merck/eg5_positive/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/eg5_positive/dg_results.csv b/summaries/dec_08_2025/merck/eg5_positive/dg_results.csv new file mode 100644 index 0000000..c068acd --- /dev/null +++ b/summaries/dec_08_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) +CHEMBL1077227,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1cccs1,-8.379057914083436,0.06523791951704336,-11.394990672677858 +CHEMBL1086410,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-8.22642448816731,0.06220539492130232,-11.52802099480568 +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,-19.58625060717704,0.08153408467620164,-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,-16.780542261550604,0.08534949534982052,-10.781167858036888 +CHEMBL1082248,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-9.075001844826227,0.06719267777204792,-11.699526909017699 +CHEMBL1085666,[NH3+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-8.01547012024793,0.0715335912380064,-10.568530825025436 +CHEMBL1082249,CC(=O)NCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-8.480320876275885,0.05672698502371304,-11.286296985191486 +CHEMBL1085692,C[NH+](C)CCCC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-4.716502415610146,0.06763349528112769,-11.394990672677858 +CHEMBL1084935,CC[N@H+](CCO)C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-7.325824759797026,0.071629348051152,-10.599110079658544 +CHEMBL1096002,OCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Cl)cc(F)c1N[C@H]2c1ccccc1,-9.36108976062724,0.03761390148688028,-11.1943977818631 +CHEMBL1083517,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccc(O)cc1,-11.01257678753342,0.05752448936903758,-11.52802099480568 +CHEMBL1083836,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C3CC3)ccc1N[C@H]2c1ccccc1,-9.176399739611602,0.05453256205191589,-10.924940178206626 +CHEMBL1096003,C[NH+](C)CCS(=O)(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(Cl)cc(F)c1N[C@H]2c1ccccc1,-14.333260506538123,0.06699911237140678,-11.941250918631892 +CHEMBL1084143,CC(C)c1ccc2c(c1)[C@H]1O[C@@H](CNS(=O)(=O)CCC[NH+](C)C)CC[C@H]1[C@H](c1ccccc1)N2,-16.795573023603506,0.0803649074018443,-11.941250918631892 +CHEMBL1084431,Cc1ccc(C(=O)N(CC[NH3+])C[C@H]2CC[C@@H]3[C@H](O2)c2cc(C(F)(F)F)ccc2N[C@H]3c2ccccc2)cc1,-9.547109420980561,0.08182496754940018,-9.865858249826928 +CHEMBL1084677,C[NH2+]CCS(=O)(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-16.316590366603883,0.0629639381911902,-11.52802099480568 +CHEMBL1084678,CN(C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1)S(=O)(=O)CCC[NH3+],-16.120770355285597,0.07807456619267485,-11.1943977818631 +CHEMBL1086409,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccc(F)cc1,-9.413483384616317,0.05171223834787821,-9.933787802066142 +CHEMBL1093087,[NH3+]CCN(C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1)c1ccccc1,-8.356213135294661,0.08298219482415671,-10.599110079658544 diff --git a/summaries/dec_08_2025/merck/hif2a/README.md b/summaries/dec_08_2025/merck/hif2a/README.md new file mode 100644 index 0000000..7057dc5 --- /dev/null +++ b/summaries/dec_08_2025/merck/hif2a/README.md @@ -0,0 +1,38 @@ +# Hif2A Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.72 +- RMSE: 2.17 +- R²: 0.03 +- Kendall 𝜏: 0.10 +- Spearman ρ: 0.13 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 14.35 Hours +- Total Nanoseconds Simulated: 7982.80 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/hif2a/ddg_results.csv b/summaries/dec_08_2025/merck/hif2a/ddg_results.csv new file mode 100644 index 0000000..4f83bd4 --- /dev/null +++ b/summaries/dec_08_2025/merck/hif2a/ddg_results.csv @@ -0,0 +1,76 @@ +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) +155,231,-19.664685200259424,0.05097673071941284,-21.942874463036958,0.05197439206220043,2.2781892627775324,0.07280085511225023,0.48344801922838815 +155,23,-1.21452364559464,0.04706112768588036,-1.9315702899072775,0.049487424136775274,0.7170466443126376,0.06829168973425552,3.4572146912983386 +155,163,-17.789316342588748,0.053912743075052776,-19.633814250292975,0.052625861733656666,1.8444979077042254,0.0753396654431555,-0.5101179827265295 +156,163,-19.49717940120303,0.0586963556807828,-21.89922496713449,0.0574654260205492,2.4020455659314606,0.08214339509618637,-1.2819886962574638 +156,165,-16.16159274788522,0.05679627040813467,-19.641776640628894,0.058261734612844424,3.480183892743675,0.08136489447158073,0.5039613211752002 +156,164,-15.384745436649709,0.06406646586712082,-21.049705957245525,0.06648739252520842,5.664960520595817,0.09233138910199552,2.9898802141072442 +156,231,-21.681839120559076,0.054671778948719406,-23.99017150885015,0.05480761956650435,2.3083323882910727,0.0774136846814845,-0.2884226943025462 +156,215,-15.745496183567049,0.05734203447887912,-16.18567746872959,0.05778203425914728,0.44018128516254057,0.08140560423768275,-0.8687587724312539 +156,289,-19.19710303236415,0.05713365214726969,-21.468465945742476,0.057168213322430286,2.2713629133783253,0.08082362787059306,-1.1851006373571475 +156,57,13.995948683339158,0.04723761697995563,14.786663190850263,0.04655548514099369,-0.7907145075111048,0.0663234924793491,-0.9433766277429518 +156,290,17.015925985871515,0.05613272738943301,17.899010773046673,0.05626283813144053,-0.883084787175159,0.07947571980662446,-0.8346829402565787 +15,163,-20.37116753324166,0.04459581948965857,-23.30512978309093,0.04380811986934333,2.9339622498492717,0.06251350640014497,0.0361422632275048 +156,336,-39.423693300155286,0.064635548341797,-40.32396205733229,0.06733951083583417,0.9002687571770042,0.09334004408105989,-0.08782980348778785 +165,15,16.5926407643093,0.04806489240465973,21.032834752011176,0.04936378336945271,-4.4401939877018775,0.06889859933567426,-1.8220922806601687 +165,290,34.188626331626494,0.04813882171736296,37.61299131606284,0.047974551730844035,-3.4243649844363437,0.06796251739092282,-1.3386442614317788 +167,231,-13.744640725604693,0.053265371909423175,-14.58193724195334,0.05494233379843188,0.8372965163486481,0.07652359040104872,0.6549539334404056 +167,252,-34.22503720984126,0.057526291181213864,-34.869496633925245,0.05985307774031685,0.6444594240839898,0.08301605321896613,0.9673865072313318 +167,290,26.06851450571037,0.05540375478008451,27.3452863477896,0.05616606070364006,-1.2767718420792267,0.07889361456224907,0.10869368748637306 +1,23,-2.20145125192781,0.05097315881439289,-3.932993953771513,0.051678902106760946,1.731542701843703,0.07258768382086249,4.28367453895076 +167,57,22.139847677217226,0.05780856177870551,24.038422471193723,0.05804216022220346,-1.8985747939764976,0.08191899766343794,0.0 +1,256,-39.8476720592189,0.06636131654898221,-42.85839877714905,0.06772002092227954,3.0107267179301447,0.09481469067517015,0.654953933440404 +1,224,13.103111763253047,0.07254572738746697,10.22005759878343,0.0715170348480824,2.883054164469617,0.10187035307506549,1.674866888824337 +1,7a,5.658727832954046,0.05136081965482659,4.5662152715770015,0.050831341733585875,1.092512561377045,0.07226174020913287,1.3358321582844292 +1,54,-17.727331900761026,0.07026199786867741,-20.80895210074182,0.0717929648934762,3.0816201999807924,0.10045386081527148,2.0276740270468614 +1,7b,10.905454904976171,0.058257318349014105,4.9398111672355975,0.06022293165311809,5.965643737740574,0.08378971678025,3.954550704058438 +1,67,1.6103360259873023,0.0757110787292016,1.37965146852093,0.07494069500281551,0.2306845574663722,0.1065282836144673,1.1600830605950025 +206,251,-6.233974848714116,0.049234824034772015,-7.340924344330526,0.05115516764398921,1.10694949561641,0.07099943009925928,-0.12137852266450505 +1,84,-2.418750938084841,0.055344865351142865,-3.407996767805265,0.055681239295059394,0.9892458297204236,0.07850767179180516,3.7724929256800914 +206,155,12.279940371845678,0.05376887665215757,14.28847079209621,0.05301148310868998,-2.0085304202505316,0.07550701581851754,-0.38265066919310436 +206,254,-5.950213323876224,0.04207675612729848,-8.32759321822155,0.047612776495010466,2.3773798943453253,0.06354077345893715,0.5768395005871398 +215,15,16.58524280681772,0.045978876558004624,17.54981290549856,0.04519083890254049,-0.9645700986808403,0.06446913222815702,-0.4493721870537147 +227,15,-10.82491357038651,0.04706841415255602,-12.381460588840087,0.04880003812523404,1.5565470184535763,0.06780029005735029,-0.28944265137229913 +215,57,29.476106832064357,0.05725253297429193,30.90270350530688,0.0567559194967712,-1.4265966732425241,0.08061691466371283,-0.07461785531169793 +227,61,-23.434825576643803,0.056628132463875366,-24.90186832222021,0.05531563204124348,1.4670427455764063,0.0791616354964225,0.654953933440404 +224,25,-8.684406973819199,0.06691390633504445,-6.911860392078286,0.06572643411047051,-1.7725465817409125,0.09379464271424633,-0.6268939420388322 +234,156,18.036047382776513,0.06355390588901719,21.618904698335687,0.06366701696837736,-3.5828573155591754,0.08995881281676467,0.6154583842864613 +234,289,-0.41495565165836285,0.052689439907791076,0.2984991147942181,0.05466807968870558,-0.7134547664525809,0.07592612208355824,-0.5696422530706864 +235,15,-11.891383688749418,0.047658466179281385,-10.371663393023434,0.04725104678081357,-1.5197202957259839,0.06711177855223582,-0.9289109151471386 +234,266,37.20960232236181,0.0750611947806007,41.883457767673455,0.0749024643019737,-4.673855445311648,0.10604037966925489,-0.1869915838775803 +235,25,-9.498083559184169,0.04785522230800649,-8.918023268722157,0.048144461710357765,-0.5800602904620105,0.0678823356664223,-0.16113757006002102 +237,164,-19.547809071140104,0.05042912906148509,-21.353514292833104,0.05077375832288738,1.8057052216929996,0.07156166286588718,2.8022607578579346 +235,224,-0.7635729813830353,0.06617245348929443,-1.5777837897211877,0.06274106364663296,0.8142108083381525,0.09118790856414945,0.4657563719788112 +237,227,6.502329725429146,0.056844854299841395,11.77683387193693,0.058106613967163864,-5.274504146507785,0.08128785916174198,-1.2163077643619793 +254,251,-0.02527148367710831,0.0339355480857233,0.9797756869484674,0.03251176364153046,-1.005047170625576,0.046996129616822487,-0.6982180232516448 +237,289,-26.053211019614412,0.06076448560695386,-23.309107822926347,0.06219158956413601,-2.7441031966880662,0.08694893054886675,-1.3727200936064574 +251,256,-21.24577305879839,0.055556310516821285,-19.706593946030683,0.053591082309285124,-1.53917911276771,0.07719137089935661,-0.4327780607406168 +252,336,2.4255662334551853,0.046805093957312055,4.561569069149954,0.04661834670423856,-2.1360028356947685,0.06606048039326841,-0.11183968297616778 +252,254,22.598630259573312,0.05622622348407863,19.47218424102337,0.05408400709984882,3.126446018549943,0.07801581910906308,0.16360957676092994 +30,31,10.17071597331961,0.047566968435580094,9.96759087152969,0.04685970738924112,0.20312510178991808,0.06677161569676722,1.7340769005913148 +30,50,-11.943445194039962,0.05583404645972134,-14.590035211761187,0.05312515564713408,2.646590017721224,0.07706959781002197,0.8741784894105249 +31,50,-22.150454948945665,0.05381288484464836,-24.4298809126824,0.05307479908018756,2.2794259637367373,0.07558280804988436,-0.8598984111807898 +266,15,-18.06883840863877,0.06895090008291188,-18.82121216762895,0.06889496296837636,0.7523737589901792,0.09747175254737982,-0.515680991320927 +30,124,12.983333159247572,0.06939309493051175,14.426061902451941,0.06954176127478595,-1.442728743204369,0.0982418352090103,0.4454628959187488 +266,155,-21.05390619718137,0.0726355000187565,-22.057833231191097,0.07092685049453233,1.0039270340097275,0.10152110117629987,0.030579254633107233 +338,336,-0.26608799527453364,0.04530236453333053,1.0731810838649394,0.041385720942662345,-1.339269079139473,0.061360265076470175,0.9408585046248816 +338,15,40.63290822619465,0.06259683933043593,42.43317766788531,0.062120002738358056,-1.800269441690659,0.08818876932112174,-0.28944265137229913 +41,35,-3.5342683135115034,0.04050465044228544,-3.8309578602530925,0.0414405204962276,0.296689546741589,0.05794776480978359,2.6490753093570083 +41,42,-1.0321080113477412,0.04043751396513826,-1.7299948067382318,0.03966963080032216,0.6978867953904905,0.056646907625347215,0.8525734277580141 +42,35,-2.777211424466375,0.047352282348539325,-1.9813878980844555,0.04818507614621598,-0.7958235263819194,0.06755768059097662,1.7965018815989942 +43,42,-1.3947470265178579,0.03924518975849719,-1.5422728154941174,0.039805515009484115,0.14752578897625956,0.05589869358357776,-0.24172400961419235 +35,84,2.687974162578734,0.0663258476234096,0.40509107645598724,0.06696358164715628,2.2828830861227467,0.09425093808540642,-0.42378178799254007 +43,31,8.319283983947518,0.050870789500259764,6.850447138741448,0.04985925548028183,1.4688368452060705,0.07123048912809565,-0.1437723201697379 +43,41,-0.5249441877887314,0.04492085896074343,0.28400501581796284,0.04569303686533982,-0.8089492036066942,0.0640760266226637,-1.0942974373722065 +338,67,39.27959157455772,0.07511965721956333,40.71969922872886,0.07445109457142013,-1.4401076541711353,0.10576354940936522,0.5904408075243162 +61,23,7.278401703617894,0.05594751521373181,7.072749443791367,0.056948315926149316,0.20565225982652674,0.07983254440023357,3.0590783524396694 +61,25,13.77558212248459,0.05621737980446458,14.277772174947572,0.05494872570142729,-0.5021900524629814,0.07861142568539332,-0.1766232397255855 +61,7a,14.823611200793025,0.054871015417674404,15.668844465747874,0.05534607167423866,-0.8452332649548496,0.07793597361127033,0.11123597177333892 +50,124,25.217855640824368,0.06947825448448351,28.80065592175896,0.06859788853552094,-3.5828002809345887,0.09763656158295625,-0.42871559349177607 +54,35,12.356199802977452,0.06380154557408427,16.94261705598307,0.06323754867881755,-4.586417253005621,0.0898310902780756,2.16860068662577 +54,124,27.433875021222963,0.06415588776345703,31.43193096531095,0.0638259821010856,-3.998055944087987,0.09049714871688165,-0.8185635102013356 +7b,7a,-4.750303742405394,0.049766695514225745,-0.5194475801550317,0.05140694641758278,-4.230856162250362,0.07154996940869984,-2.618718545774009 +61,84,7.174117658931285,0.0588983949631411,7.549824444019133,0.05896536939080671,-0.37570678508784705,0.0833422804861281,2.547896739169001 +7b,164,-22.172833322124653,0.06510572388481438,-23.8358856179839,0.0637594854768839,1.6630522958592489,0.09112643563117487,0.633660071232162 +67,256,-41.14047910336048,0.07198902578251436,-43.177123044546995,0.0726011400699145,2.0366439411865214,0.10224160294404065,-0.5051291271545986 +84,50,-14.118175844957602,0.06630434068142652,-15.301638516677732,0.06792053453251234,1.1834626717201313,0.09491819954245272,-2.1346668153427895 diff --git a/summaries/dec_08_2025/merck/hif2a/dg_plot.png b/summaries/dec_08_2025/merck/hif2a/dg_plot.png new file mode 100644 index 0000000..2267df1 Binary files /dev/null and b/summaries/dec_08_2025/merck/hif2a/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/hif2a/dg_results.csv b/summaries/dec_08_2025/merck/hif2a/dg_results.csv new file mode 100644 index 0000000..d9e0d50 --- /dev/null +++ b/summaries/dec_08_2025/merck/hif2a/dg_results.csv @@ -0,0 +1,43 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +155,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)F)c3c2CC[C@H]3O)c1,-10.527422467411066,0.046897545051539355,-10.568530825025436 +231,CS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)[C@H](F)C2,-8.414914773050226,0.06400177305329369,-10.085082805797049 +23,O=S(=O)(c1ccc(Oc2cc(F)cc(F)c2)c2c1[C@H](O)[C@H](O)C2)C(F)F,-9.919209154222697,0.05019857091874759,-7.111316133727097 +163,CS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-8.38464458354345,0.0499560050554435,-11.078648807751966 +156,N#Cc1cccc(Oc2ccc(S(=O)(=O)C(F)F)c3c2CC[C@H]3O)c1,-10.696175475589966,0.038494243235698965,-9.796660111494502 +165,CS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](N)C(F)(F)C2,-7.1408744648848135,0.05523345805203905,-9.292698790319301 +164,CS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@@H](N)C(F)(F)C2,-4.7077890527828865,0.0597981377194804,-6.8067798973872575 +215,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)CCl)c3c2CC(F)(F)[C@H]3O)c1,-10.175995786217074,0.054448030240719196,-10.665418883925756 +289,CS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)[C@H](F)[C@@H]2F,-8.535545272803507,0.06379212009629961,-10.981760748851649 +57,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)(F)F)c3c2CC[C@H]3O)c1,-11.484888481218809,0.055602509522460423,-10.740036739237453 +290,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)(F)F)c3c2CC(F)(F)[C@H]3N)c1,-10.917022493125344,0.05324235646715472,-10.631343051751081 +15,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)F)c3c2CC(F)(F)[C@H]3O)c1,-11.165665713660156,0.03850257342760638,-11.11479107097947 +336,N#Cc1cc(F)cc(Oc2ccc(S(N)(=O)=O)c3c2[C@@H](F)[C@@H](F)[C@H]3O)c1,-10.585183941962915,0.06192435877697871,-9.88448991498229 +167,N#Cc1cc(Cl)cc(Oc2ccc(S(=O)(=O)CF)c3c2CC(F)(F)[C@H]3O)c1,-9.46172336236413,0.06575389193652705,-10.740036739237453 +252,N#Cc1cc(F)cc(Oc2ccc(S(N)(=O)=O)c3c2CC(F)(F)[C@H]3O)c1,-8.738213606886278,0.06823990625471411,-9.772650232006121 +1,O=S(=O)(c1ccc(Oc2cc(F)cc(Cl)c2)c2c1[C@H](O)CC2)C(F)F,-11.735881628254283,0.0356814496439296,-11.394990672677858 +256,NS(=O)(=O)c1ccc(Oc2cc(F)cc(F)c2)c2c1[C@H](O)C(F)(F)C2,-8.73518729040465,0.05460067975073628,-10.740036739237453 +224,Cn1cc(Oc2ccc(S(=O)(=O)C(F)(F)F)c3c2CC(F)(F)[C@H]3O)cn1,-8.849583928710773,0.06320500464467156,-9.72012378385352 +7a,C[C@H]1C[C@@H](O)c2c(S(=O)(=O)C(F)F)ccc(Oc3cc(F)cc(Cl)c3)c21,-10.686477814789553,0.05262914184453867,-10.05915851439343 +54,CS(=O)(=O)c1ccc(Oc2cc(F)cc(Cl)c2)c(C(F)F)c1CO,-8.694687762442706,0.0781186052886584,-9.367316645630996 +7b,C[C@H]1C[C@H](O)c2c(S(=O)(=O)C(F)F)ccc(Oc3cc(F)cc(Cl)c3)c21,-6.220279292523473,0.061688753407914756,-7.44043996861942 +67,N#Cc1ccc(Oc2cc(F)cc(F)c2)c2c1[C@H](O)C(F)(F)C2,-11.010326735231008,0.0616884616304205,-10.234907612082855 +206,CCS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-8.33039759117046,0.06450255763568365,-10.185880155832331 +251,CNS(=O)(=O)c1ccc(Oc2cc(F)cc(F)c2)c2c1[C@H](O)C(F)(F)C2,-7.0667129667805275,0.06104698419216799,-10.307258678496837 +84,O=C1OCc2c(S(=O)(=O)C(F)F)ccc(Oc3cc(F)cc(Cl)c3)c21,-10.639374614490823,0.051343928025699356,-7.622497746997766 +254,CNS(=O)(=O)c1ccc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-5.945067845047231,0.06350358605708839,-9.609040655245192 +227,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)(F)F)c3c2C[C@@H](F)[C@H]3O)c1,-12.098122807847988,0.050108423948599386,-10.825348419607172 +61,O=S(=O)(CF)c1ccc(Oc2cc(F)cc(Cl)c2)c2c1[C@H](O)CC2,-10.170616009468398,0.04638411886983944,-10.170394486166767 +25,O=S(=O)(c1ccc(Oc2cncc(Cl)c2)c2c1[C@H](O)C(F)(F)C2)C(F)F,-10.515403954504414,0.052845528080733464,-10.347017725892353 +234,CS(=O)(=O)c1ccc(Oc2cc(Cl)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-7.446572388210397,0.0703276899056742,-10.412118495780962 +235,N#Cc1cncc(Oc2ccc(S(=O)(=O)C(F)(F)F)c3c2CC(F)(F)[C@H]3O)c1,-9.762072504066607,0.05627796453013075,-10.185880155832331 +266,O=S(=O)(c1ccc(Oc2ccc(F)c3[nH]ncc23)c2c1[C@H](O)C(F)(F)C2)C(F)(F)F,-11.851008944760858,0.0574091308858106,-10.599110079658544 +237,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)F)c3c2CC(F)(F)[C@@H]3O)c1,-6.412061547001518,0.06040031076402434,-9.609040655245192 +30,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)F)c(Cl)c2C#N)c1,-11.596094436344707,0.08763326926192427,-10.631343051751081 +31,Cc1c(S(=O)(=O)C(F)F)ccc(Oc2cccc(C#N)c2)c1C#N,-11.354029662963418,0.08035605334852836,-8.897266151159766 +50,Cc1c(S(C)(=O)=O)ccc(Oc2cc(F)cc(Cl)c2)c1C#N,-9.141464270713369,0.08161627613566637,-9.757164562340556 +124,O=S(=O)(c1ccc(Oc2cc(F)cc(Cl)c2)c(C(F)F)c1)C(F)(F)F,-12.811202462781337,0.09307320880383015,-10.185880155832331 +338,N#Cc1cc(F)cc(Oc2ccc(S(N)(=O)=O)c3c2[C@@H](F)C(F)(F)[C@H]3O)c1,-9.337637849098801,0.05502732432783787,-10.825348419607172 +41,O=S(=O)(c1ccc(Oc2cc(F)cc(Cl)c2)c(Cl)c1CO)C(F)F,-13.42646034927864,0.07114685761718847,-9.847791268362235 +35,N#Cc1c(Oc2cc(F)cc(Cl)c2)ccc(S(=O)(=O)C(F)F)c1CO,-13.196711966625024,0.08005894657897021,-7.198715959005226 +42,N#Cc1cc(F)cc(Oc2ccc(S(=O)(=O)C(F)F)c(CO)c2Cl)c1,-12.585151512892889,0.0795296822604627,-8.995217840604221 +43,N#Cc1cccc(Oc2ccc(S(=O)(=O)C(F)F)c(CO)c2Cl)c1,-12.719170417250357,0.08127677141391661,-8.753493830990028 diff --git a/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/README.md b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/README.md new file mode 100644 index 0000000..ac2837c --- /dev/null +++ b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/README.md @@ -0,0 +1,38 @@ +# Hif2A Jmc 2023 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.09 +- RMSE: 1.34 +- R²: 0.38 +- Kendall 𝜏: 0.42 +- Spearman ρ: 0.62 + +## System Details +- Ligands: 38 +- Host Atoms: 1937 +- Map Details: + - Edges: 68 + - Min Dummy Atoms: 0 + - Max Dummy 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 12.62 Hours +- Total Nanoseconds Simulated: 6902.20 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/hif2a_jmc2023_jmc/ddg_results.csv b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/ddg_results.csv new file mode 100644 index 0000000..32b9166 --- /dev/null +++ b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/ddg_results.csv @@ -0,0 +1,69 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),exp_ddg (kcal/mol) +19a-bindingpose2,19c-bindingpose2,-2.969413594722135,0.04662610089869857,-3.860644351959636,0.042747410593465776,0.8912307572375007,0.0632561016619106,-0.02433663464145134 +19a-bindingpose1,19a-bindingpose2,1.355762384206605,0.04471425958850748,0.17552830780013715,0.044070079701839335,1.180234076406468,0.06278166082125342,0.0 +19a-bindingpose1,19c-bindingpose2,-2.4951581398126668,0.04938662321404189,-3.9677969764468437,0.04631382218327606,1.472638836634177,0.06770530760368686,-0.02433663464145134 +19a-bindingpose1,19d-bindingpose2,-1.8757019228760727,0.054179637380138264,-3.460873784250678,0.05102713704866057,1.5851718613746055,0.07442581421809279,0.3163418649258903 +19a-bindingpose2,19d-bindingpose1,-3.490739014673563,0.05262748126777124,-3.4276628108764067,0.05167201580679631,-0.06307620379715626,0.07375397617842323,0.3163418649258903 +19a-bindingpose1,19d-bindingpose1,-3.04088094965836,0.0567381589000719,-3.4464401464597976,0.05406811863958451,0.40555919680143776,0.07837461405706567,0.3163418649258903 +19c-bindingpose2,19b,-0.6088429852627834,0.03667111338090713,0.6414552085930638,0.032287906613568236,-1.2502981938558473,0.048859794003678014,-0.05187311684135094 +19c-bindingpose1,19d-bindingpose1,1.2979056324682727,0.044030339882265714,0.3637601773728627,0.04279439072375272,0.9341454550954101,0.061400575791803864,0.34067849956734164 +19c-bindingpose1,19d-bindingpose2,2.0306974206346333,0.048256915567762036,0.22942428288822045,0.043765025950595185,1.8012731377464126,0.06514681417053626,0.34067849956734164 +19d-bindingpose2,19b,-1.0466117427198147,0.04648089007523329,0.21535480028215165,0.04490219963382958,-1.2619665430019662,0.064627244054982,-0.39255161640869257 +22a,22d-bindingpose2,-0.6561368975163483,0.051425797286960014,-1.835261974454519,0.04993500821131131,1.179125076938171,0.0716806645593024,-0.007226328015077889 +22b-bindingpose1,22b-bindingpose2,0.9030452506167279,0.045733137083741875,-0.06332068220336297,0.04438914832196584,0.9663659328200909,0.06373316496354005,0.0 +22a,22f-bindingpose1,-3.1010747527952356,0.06245862264583146,-4.084348637915666,0.06171410218412094,0.9832738851204305,0.08780495402428323,-0.8193200645691765 +22b-bindingpose1,22d-bindingpose2,-1.8659865799114084,0.04367352689428154,-3.305077960369366,0.04035033715385407,1.4390913804579575,0.059460294817762466,-0.007226328015077889 +22a,22f-bindingpose2,-3.8935232982070396,0.0633690649688548,-3.9337006768901204,0.06173649584235323,0.04017737868308103,0.0884705222880471,-0.8193200645691765 +22b-bindingpose1,22d-bindingpose1,-0.5093864156072572,0.053488223596126275,-3.2552272520570176,0.052867529406356376,2.7458408364497604,0.07520615486116249,-0.007226328015077889 +22a,35l,-13.435451967837562,0.06786466477723943,-11.498941960905105,0.065133555147471,-1.9365100069324557,0.09406376949429429,-1.3585250238984485 +22b-bindingpose1,22e-bindingpose1,-3.451533135891734,0.05076858255495067,-5.225331504559299,0.05208365615547998,1.7737983686675651,0.07273346006592228,-0.49798934407135187 +22b-bindingpose1,22e-bindingpose2,-5.062843091243458,0.047694221026156954,-5.306375725407021,0.04663878408556309,0.24353263416356336,0.06670768246815119,-0.49798934407135187 +22d-bindingpose1,22f-bindingpose1,-4.58795899402869,0.052889464521847306,-2.2143069090758765,0.052810674203578836,-2.373652084952814,0.07474130562978074,-0.8120937365540986 +22e-bindingpose1,22d-bindingpose1,3.4888106252579987,0.04120231988707519,1.995804374915589,0.03899088870182056,1.4930062503424097,0.05672671827132811,0.490763016056274 +22b-bindingpose2,35l,-16.678251461055826,0.06482418994885593,-13.154623899165177,0.06402707672118603,-3.523627561890649,0.09111334784753546,-1.3585250238984485 +22e-bindingpose1,22f-bindingpose1,-0.8751834918337043,0.042525328550910214,-0.1736141649187372,0.043237750221405795,-0.7015693269149671,0.060645746863003815,-0.32133072049782463 +22b-bindingpose1,35l,-17.008576224505944,0.06746785230978083,-12.756078386787815,0.06538506739942058,-4.252497837718131,0.09395274415428839,-1.3585250238984485 +22e-bindingpose2,22f-bindingpose2,-0.44037435152784676,0.04179843148353687,-0.18192584012921734,0.041535917175489656,-0.25844851139862945,0.05892657541460443,-0.32133072049782463 +22d-bindingpose2,35c,3.6450607070738092,0.08094860260436627,4.910073994439289,0.07865178266324613,-1.2650132873654791,0.11286620034229078,-0.4744287131344549 +22g-bindingpose1,22b-bindingpose2,3.3113452516515096,0.05152399916896687,3.713257626832513,0.049311725586704346,-0.4019123751810032,0.0713187827342989,1.298524900320157 +22g-bindingpose1,22g-bindingpose2,-0.687879346664029,0.04872886711653033,-0.022558276315557447,0.047394943875501555,-0.6653210703484714,0.06797634291003314,0.0 +22g-bindingpose1,22a,0.5206844990660329,0.05898704557035443,2.0639363350617494,0.05787876993607881,-1.5432518359957166,0.08264032644195332,1.298524900320157 +22e-bindingpose2,35c,5.644208651748874,0.08145579368025697,6.873689808382808,0.07938953683887601,-1.2294811566339343,0.11374420813198288,0.016334302921819074 +22g-bindingpose2,22b-bindingpose1,3.3675349117926605,0.050917871010574905,3.5705755342945653,0.04968318376729504,-0.2030406225019048,0.07114104537820873,1.298524900320157 +22f-bindingpose2,35c,4.3712741803106425,0.0833840640922463,6.956931907790435,0.08016858268870626,-2.5856577274797923,0.11567153407323588,0.33766502341964366 +35b,35k,-4.9746292040529605,0.05376386173062573,-3.9504450673245426,0.0524607776693933,-1.024184136728418,0.07511781427775542,-0.664973745128891 +22g-bindingpose2,22a,1.4415319822898178,0.0591698804953179,2.1500665579544758,0.05774734774175012,-0.708534575664658,0.08267908398764959,1.298524900320157 +35b,35l,-4.107348961661578,0.0567202132737489,-2.0851217561795155,0.05456203994434154,-2.022227205482062,0.07870323244128848,-1.8200258496073407 +35d,35k,-1.5189363723283462,0.04035541431158548,-1.7390386674906708,0.04081382975812924,0.22010229516232457,0.057396238237233575,0.364734520053528 +35b,35o,-5.131311429068757,0.06109652545727627,-4.141142526396519,0.061324807664573856,-0.9901689026722378,0.08656510531414252,-1.340487121513917 +35e,35g,17.441458049041376,0.057746313157144215,17.040100172500356,0.055878941418531884,0.4013578765410201,0.08035603759082877,0.1222434698773103 +35c,19a-bindingpose1,-2.4864090354186197,0.07465795812131171,-4.821646710176205,0.07352090178886135,2.335237674757585,0.1047813614661068,0.5927381697578614 +35c,19b,-7.023050258595069,0.07447798317946269,-7.901285556164979,0.07269125980284388,0.8782352975699094,0.10407203865690762,0.5165284182750591 +35e,35i,0.9261192760853226,0.04719658577207708,1.018081074476998,0.04826117742202021,-0.09196179839167525,0.06750302922610764,0.020210910481112433 +35e,35h-R,25.501485918375863,0.0653952055419837,23.4952045476291,0.06523524172397073,2.006281370746764,0.0923697443466376,0.8851463502177305 +35c,19c-bindingpose1,-34.16725587440184,0.08950722539136988,-32.9734487063406,0.08799951138935552,-1.1938071680612463,0.12552074490707424,0.56840153511641 +35e,35h-S,24.779475032777867,0.06770809985227574,23.435519606303693,0.06641138223782439,1.3439554264741744,0.09484122772478305,0.8851463502177305 +35e,35j-R,5.224261473883705,0.04761074073048314,5.2247821959820415,0.046337152194275914,-0.0005207220983370712,0.06643729604958931,-0.22151309913308162 +35e,35r,-0.5435557389304071,0.04569648472077406,-1.1294534099873172,0.047229966449894675,0.5858976710569102,0.0657178700711923,-0.3254564446581652 +35e,35n,17.196563225487388,0.060575345511718795,16.580396894332477,0.06083725401615449,0.616166331154911,0.08585187219909776,0.0511874758665789 +35f,35d,7.904884564905275,0.053197770046155904,7.2828504373311,0.054016790022907095,0.6220341275741745,0.0758143544605012,0.03847559208419482 +35f,35l,5.568861905985286,0.05467013541226668,5.8384467995860705,0.05452214328348868,-0.2695848936007846,0.07721067163430742,-0.7518419923407269 +35e,35s,1.6713298032351762,0.06256375856722012,-0.0019171022393071134,0.06114878262136974,1.6732469054744834,0.08748369849367903,0.5421345217936937 +35f,35o,5.341344786854318,0.06126141601231281,5.017071652531901,0.05946899958142689,0.32427313432241694,0.08537870345144279,-0.272303264247303 +35g,35h-S,8.022371738832947,0.052304331263742565,6.398205959989053,0.050395960384521356,1.6241657788438932,0.07263260901293277,0.7629028803404201 +35g,35n,0.4619152939921673,0.04317474462352083,-0.6131000166716277,0.042662690612421436,1.075015310663795,0.06069731249073087,-0.07105599401073141 +35i,35m,-2.995893316930842,0.03960600587685099,-2.1639461360015884,0.03981231721434606,-0.8319471809292537,0.05615742429539367,0.12179673717611472 +35h-S,35n,-8.080292085091228,0.05951825304281059,-6.941841148427278,0.056114675868331125,-1.1384509366639517,0.08180024017737292,-0.8339588743511516 +35i,35q,-0.482687296831236,0.058277554875625706,-2.218297387980519,0.05689076711455778,1.7356100911492827,0.08144220518358043,-0.36003346623759713 +35h-R,35q,-24.519938321877305,0.07076622254050352,-24.060721914293985,0.0698816658073728,-0.45921640758332083,0.09945504244966871,-1.224968905974215 +35j-R,35q,-4.418330171203384,0.05732894142042921,-6.1685171455486385,0.056317187427987137,1.7501869743452545,0.08036313286691875,-0.1183094566234031 +35j-R,35r,-5.08035366566035,0.04758318710510489,-6.371283201642539,0.0475328233460533,1.2909295359821904,0.06725718541781636,-0.1039433455250836 +35h-R,35r,-25.94758523478687,0.06951518110362623,-24.133890617470346,0.07027242700096324,-1.8136946173165251,0.09884621591379036,-1.2106027948758957 +35j-S,35q,-4.811613020045234,0.04822526664360568,-6.257853928441959,0.04666665790759604,1.4462409083967247,0.06710777379045935,-0.1183094566234031 +35l,35m,-0.7376141309248582,0.032716646126538705,-0.04647093922973819,0.03285188385246206,-0.6911431916951198,0.046364050798272764,0.0471788818644185 +35k,35m,0.686384888895563,0.042972699738891076,1.8289964287375955,0.04268093930961431,-1.1426115398420325,0.060566620371289244,-1.1078732226140313 +35j-S,35s,-3.470773486406618,0.0550866033944319,-5.00668930627142,0.054135240909300296,1.5359158198648022,0.07723443650240103,0.7636476209267753 +35s,35o,-5.4865028792900175,0.04572196487004574,-4.38469193809205,0.044897174180508766,-1.101810941197967,0.06408006180531227,0.03223297209253893 +35j-S,35t,-3.387228063199969,0.05746307019421752,-5.809878598041363,0.05732440027011516,2.4226505348413947,0.08116705798828702,0.9097809927443413 +35t,35d,-2.2361277450241457,0.05512145925896338,-1.0421552156631804,0.05358219183049135,-1.1939725293609653,0.07687279461680273,0.1968784566064707 +35t,35o,-5.382398036695548,0.05645895858342651,-4.213353209675836,0.05485930508556091,-1.1690448270197118,0.07872202588091672,-0.11390039972502713 diff --git a/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/dg_plot.png b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/dg_plot.png new file mode 100644 index 0000000..76483d2 Binary files /dev/null and b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/dg_results.csv b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/dg_results.csv new file mode 100644 index 0000000..a78fa14 --- /dev/null +++ b/summaries/dec_08_2025/merck/hif2a_jmc2023_jmc/dg_results.csv @@ -0,0 +1,39 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +19a-bindingpose2,CS(=O)(=O)c1sc(Oc2cccc(F)c2)c2c1[C@H](O)C(F)(F)C2,-7.485694082845032,0.10238885514910856,-8.236320561638735 +19c-bindingpose2,CS(=O)(=O)c1sc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-6.776686441687031,0.1047002211100184,-8.260657196280185 +19a-bindingpose1,CS(=O)(=O)c1sc(Oc2cccc(F)c2)c2c1[C@H](O)C(F)(F)C2,-8.281307079848608,0.09980841721781314,-8.236320561638735 +19d-bindingpose2,CS(=O)(=O)c1sc(Oc2cc(Cl)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-6.912281265804295,0.10268883545020663,-7.919978696712844 +19d-bindingpose1,CS(=O)(=O)c1sc(Oc2cc(Cl)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-7.831854578673582,0.09582787587959164,-7.919978696712844 +19b,CS(=O)(=O)c1sc(Oc2cc(F)cc(F)c2)c2c1[C@H](O)C(F)(F)C2,-8.11904712548027,0.10648462637717117,-8.312530313121536 +19c-bindingpose1,CS(=O)(=O)c1sc(Oc2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-8.93525619379089,0.09793239552504378,-8.260657196280185 +22a,CS(=O)(=O)c1sc(-c2ccc(F)cc2)c2c1[C@H](O)C(F)(F)C2,-8.444068163943456,0.05422057914905266,-8.347403690247063 +22d-bindingpose2,CS(=O)(=O)c1sc(-c2cccc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-7.062581276809832,0.06467925612482654,-8.35463001826214 +22b-bindingpose1,CS(=O)(=O)c1sc(-c2ccc(F)c(F)c2)c2c1[C@H](O)C(F)(F)C2,-8.100367353085614,0.053242245147396276,-8.347403690247063 +22b-bindingpose2,CS(=O)(=O)c1sc(-c2ccc(F)c(F)c2)c2c1[C@H](O)C(F)(F)C2,-7.337784055342793,0.06348682468017387,-8.347403690247063 +22f-bindingpose1,CS(=O)(=O)c1sc(-c2cc(Cl)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-7.39111092579167,0.06860679995418846,-9.166723754816239 +22f-bindingpose2,CS(=O)(=O)c1sc(-c2cc(Cl)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-7.9354155764249334,0.0633014285485858,-9.166723754816239 +22d-bindingpose1,CS(=O)(=O)c1sc(-c2cccc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-5.137887657934733,0.06831603204113153,-8.35463001826214 +35l,CS(=O)(=O)c1sc(OCC(F)(F)F)c2c1[C@H](O)C(F)(F)C2,-11.191948969357993,0.04397424208433808,-9.70592871414551 +22e-bindingpose1,CS(=O)(=O)c1sc(-c2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-6.577010831541894,0.06750131546432264,-8.845393034318414 +22e-bindingpose2,CS(=O)(=O)c1sc(-c2cc(F)cc(C#N)c2)c2c1[C@H](O)C(F)(F)C2,-7.793340636973945,0.06195953830645894,-8.845393034318414 +35c,CS(=O)(=O)c1sc(OC2CCC2)c2c1[C@H](O)C(F)(F)C2,-9.271819482834308,0.07563001467266313,-8.829058731396596 +22g-bindingpose1,CS(=O)(=O)c1sc(-c2cc(F)cc(Cl)c2)c2c1[C@H](O)C(F)(F)C2,-6.988531810908851,0.06539625240655536,-9.64592859056722 +22g-bindingpose2,CS(=O)(=O)c1sc(-c2cc(F)cc(Cl)c2)c2c1[C@H](O)C(F)(F)C2,-7.761040951024251,0.06865826117015693,-9.64592859056722 +35b,CC(C)Oc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-9.338568974456248,0.06527231470688542,-7.885902864538171 +35k,CS(=O)(=O)c1sc(OCC(F)F)c2c1[C@H](O)C(F)(F)C2,-10.428641911181254,0.06293729231804922,-8.550876609667062 +35d,CCCOc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-10.465006022933489,0.059283642456592976,-8.91561112972059 +35o,CS(=O)(=O)c1sc(OCCC(F)(F)F)c2c1[C@H](O)C(F)(F)C2,-10.445502435569297,0.054993203654362464,-9.226389986052087 +35e,CC(C)COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-11.073057769606738,0.0609100814626298,-9.800757479938321 +35g,CS(=O)(=O)c1sc(OCC2CCC2)c2c1[C@H](O)C(F)(F)C2,-11.074838272585847,0.0820668322050718,-9.67851401006101 +35i,CC(C)(C)COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-11.104964478219616,0.05846137245987043,-9.780546569457208 +35h-R,C[C@@H](Oc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O)C1CCC1,-8.89980527662051,0.07797888310673756,-8.91561112972059 +35h-S,C[C@H](Oc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O)C1CCC1,-9.409665528429507,0.08327551959214015,-8.91561112972059 +35j-R,CC[C@@H](C)COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-11.33604766544107,0.07015795756237692,-10.022270579071401 +35r,C[C@@H](COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O)C(F)(F)F,-10.352816384307836,0.071240411677331,-10.126213924596485 +35n,CS(=O)(=O)c1sc(OCC2CC(F)(F)C2)c2c1[C@H](O)C(F)(F)C2,-10.258475279602688,0.08718974285398558,-9.74957000407174 +35f,CS(=O)(=O)c1sc(OCC2CC2)c2c1[C@H](O)C(F)(F)C2,-10.938479191125984,0.06649529612353991,-8.954086721804785 +35s,CC(F)(F)CCOc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-9.433421796399843,0.065152023564465,-9.258622958144626 +35m,CC(F)(F)COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-11.8186848106825,0.045815211462790925,-9.658749832281092 +35q,C[C@H](COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O)C(F)(F)F,-9.530593152132926,0.0654447736148926,-10.140580035694805 +35j-S,CC[C@H](C)COc1sc(S(C)(=O)=O)c2c1CC(F)(F)[C@H]2O,-11.125885681412358,0.06746100971625395,-10.022270579071401 +35t,CS(=O)(=O)c1sc(OCCCC(F)(F)F)c2c1[C@H](O)C(F)(F)C2,-9.09417857372378,0.06487538122917477,-9.11248958632706 diff --git a/summaries/dec_08_2025/merck/pfkfb3/README.md b/summaries/dec_08_2025/merck/pfkfb3/README.md new file mode 100644 index 0000000..6cdd3c0 --- /dev/null +++ b/summaries/dec_08_2025/merck/pfkfb3/README.md @@ -0,0 +1,38 @@ +# Pfkfb3 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.95 +- RMSE: 1.20 +- R²: 0.31 +- Kendall 𝜏: 0.42 +- Spearman ρ: 0.57 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 18.67 Hours +- Total Nanoseconds Simulated: 7276.40 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/pfkfb3/ddg_results.csv b/summaries/dec_08_2025/merck/pfkfb3/ddg_results.csv new file mode 100644 index 0000000..7555740 --- /dev/null +++ b/summaries/dec_08_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,-1.5836855487466581,0.035610895510383496,-1.0503187264218505,0.0372894598640886,-0.5333668223248077,0.05156199856490171,-0.36593561542120234 +20,42,-3.1889803266085304,0.04911087753694665,-2.8485117368635957,0.049491850753362,-0.3404685897449347,0.06972317823681039,0.04995926363476655 +24,23,-1.3714730115108862,0.049869475217642636,-2.582402253121231,0.05135602768320134,1.210929241610345,0.0715849574832647,0.9613797585629699 +19,33,-4.046970931372296,0.04775664426840363,-0.7226105813864773,0.05045229016774652,-3.324360349985818,0.06947035810293006,-1.0626948334705881 +24,26,-7.76346513934995,0.058945427344924306,-7.841332109327835,0.0590224792555444,0.07786696997788486,0.0834159245129305,-0.3013902408500421 +20,44,-3.250922812347596,0.0645356091274549,-3.761436715512787,0.0628320663236741,0.5105139031651911,0.0900706023292518,-1.4411170427820765 +26,34,-5.94127617514843,0.04024139008385488,-4.056844709296905,0.03818288276674536,-1.8844314658515255,0.05547343519433418,-0.8079247352160092 +29,35,0.6514231819201707,0.03733040977068147,2.4306838129440393,0.03691782043015886,-1.779260631023869,0.05250223765669845,-0.49585011085754177 +24,29,-16.30837688873553,0.06961401560123459,-15.684787023266676,0.07025579646152028,-0.6235898654688549,0.0989039337163669,-0.7809289689434661 +29,57,2.5654062977410628,0.04905736103125502,4.2026349857071335,0.0495815929913086,-1.637228687966071,0.06974925831079982,-0.833515134277182 +26,37,3.7203587271178367,0.06592238521517214,5.867514029732604,0.06974091402727,-2.147155302614767,0.09596643143212429,-0.8327685283413407 +30,19,7.160422406267043,0.055107405699807946,6.818661939297788,0.052258131333717234,0.341760466969255,0.07594562827085746,1.657635726612512 +30,23,5.065839413773127,0.05424733026614848,5.90313563502956,0.050300844394491645,-0.8372962212564323,0.07397937407009775,1.2917001111913096 +26,60,-0.6862193825503111,0.07572507655139095,1.855772689902495,0.0748589188108929,-2.541992072452806,0.10648072569366664,1.0320742776147849 +30,33,3.8777802989405727,0.060971016370839244,6.087145088588317,0.05947473737025174,-2.209364789647744,0.0851745808475367,0.5949408931419238 +31,33,6.621115204803006,0.057190299197865176,5.852065321541899,0.057628095487580175,0.7690498832611072,0.08118945566923697,0.6797460613640534 +31,34,-5.775905679833215,0.05136282511873998,-6.0826056317264845,0.051696768733287574,0.30669995189326965,0.07287452024981905,-0.694189455215582 +31,37,2.4454341437842877,0.06915327787419297,3.7900298698339197,0.0674707466525881,-1.344595726049632,0.09661509972360986,-0.7190332483409135 +31,60,-2.2543698275975803,0.069724017972067,-2.4943070270849663,0.06984597917236317,0.23993719948738626,0.0986909291106093,1.145809557615212 +35,36,8.421368390401195,0.060417593792927514,7.663273407043341,0.05735993190120662,0.758094983357854,0.08330934777945542,2.7150305143650058 +35,53,3.9035464577476287,0.05357638047789304,3.587871427462961,0.05158239548188439,0.315675030284668,0.0743718499753871,3.1606807866781303 +35,33,11.616686912048944,0.07093455840238408,10.948411788217545,0.06943068983337067,0.6682751238314008,0.09925891529972992,1.5413996203145919 +37,34,-10.026290471848878,0.0650118145621939,-9.800698186282238,0.06424495442592407,-0.2255922855666385,0.09139994639964592,0.024843793125331623 +38,69,-7.5484062463492405,0.056878186790071325,-5.662757708419867,0.05680223698049248,-1.8856485379293735,0.0803842164763349,-1.9680077958110116 +38,35,-3.6099618486232123,0.06250073625904021,-2.066475531340559,0.06425258864085233,-1.543486317282653,0.08963669549895673,-1.3886187627771773 +41,20,-5.274636977895637,0.04906693705871546,-5.319863791697024,0.04830128995249395,0.045226813801387204,0.06885186216362517,-1.1357712408201242 +38,70,-10.062847430222398,0.061622977408965385,-7.611241669866049,0.06326530861270566,-2.451605760356349,0.08831698941090975,-1.5547778719848018 +41,42,-7.432971444680919,0.055693276256415354,-7.9650900255829535,0.05605678461658085,0.5321185809020352,0.07901964389772415,-1.0858119771853576 +41,44,-8.520236647233116,0.06609919195519041,-10.046618240602891,0.06619157472102682,1.5263815933697762,0.09354372101417811,-2.5768882836022007 +43,39,-1.8572444348870838,0.06141382145038903,-4.3128387919870885,0.060354392813308254,2.4555943571000043,0.08610638882802704,0.8051324322224471 +42,44,-1.8725659540375257,0.07033505550400866,-1.6986715626202433,0.07021021278364382,-0.17389439141728238,0.09938055147701949,-1.491076306416843 +43,46,6.424734205120748,0.06511752616988006,4.206708051951061,0.06578416659723914,2.218026153169686,0.09256267492557856,0.13916438074945203 +43,49,-3.2614694325230915,0.061629008543361126,-6.6196873732320745,0.06067951913231533,3.3582179407089825,0.08648779530180371,0.06376671530452503 +43,62,-78.32631121407903,0.0643108318466904,-77.72330401885455,0.06471237098108587,-0.6030071952244791,0.09123362346638969,0.30782710189406143 +44,46,6.017925741108787,0.042691272534008125,4.548366388655316,0.040780648143658484,1.469559352453471,0.059039021109685015,2.1022918823585575 +43,63,1.8149681178173809,0.06469045762047128,0.9032206789627697,0.06567017391569803,0.9117474388546113,0.09218148973228853,-0.5674751668536532 +48,47,3.7049359177908903,0.039237939264243155,3.034220969763889,0.039935477885508046,0.6707149480270015,0.05598623287602352,-0.32912383489232344 +44,39,-2.142384340776569,0.061856359990871204,-3.906776917255114,0.06126556859080074,1.7643925764785449,0.08706135288447085,2.7682599338315526 +52,53,2.7186082722780536,0.03798094664994647,2.4717832169960627,0.03682630153605316,0.24682505528199059,0.05290301308290854,3.4187390992141404 +49,47,13.818485265685073,0.05000166093654009,13.467331477967576,0.04878426166099936,0.35115378771749667,0.06985749982801827,-0.4016385393235288 +48,64,-2.4497259883098876,0.054411319891439526,-1.3312257639284937,0.05624156630158352,-1.1185002243813937,0.07825410859746584,-1.4247133928414906 +49,46,12.883239302009784,0.05580135439567847,13.363211217743261,0.05575123218998743,-0.47997191573347886,0.07887959839587164,0.075397665444927 +54,52,-3.070030214333688,0.05054883463100799,-1.8219126031003325,0.04652700676614461,-1.2481176112333556,0.06870187072540207,-2.2294486125237456 +54,35,-5.2943981566871345,0.058877906628467515,-3.2891582399572257,0.056641256069229026,-2.005239916729909,0.08169969264354984,-1.9713902999877357 +54,53,-0.19353172916895503,0.05717156865153773,0.1851064771238684,0.05742143098122902,-0.37863820629282346,0.08102967973532624,1.1892904866903946 +55,70,-6.40905938152283,0.04461015122565711,-6.0923841854488785,0.04451876375497636,-0.3166751960739522,0.06302369331170138,0.33362321294257935 +55,52,2.3991699420026475,0.05228702067181707,0.6676289344499141,0.052840647351303484,1.731541007552733,0.0743375177366035,0.24172400961419407 +55,36,8.641730038816606,0.05939694999750628,6.860834955559658,0.061930796236380176,1.7808950832569486,0.08581037927592618,3.2148128365152098 +56,35,-0.20659466476077523,0.04785748037198859,-0.9679666963542396,0.047190391122284556,0.7613720315934643,0.06721064976497003,0.42956422674802724 +56,55,-0.3518757468063276,0.034892429565019326,-0.11618443051565154,0.032783918233044496,-0.23569131629067608,0.04787762458247884,-0.07021809540217654 +56,57,1.3336680842017932,0.05433395122318183,0.6093668240514855,0.054353754063777876,0.7243012601503077,0.07685381471565841,0.09189920332838697 +58,39,-12.827616764680716,0.056961859438770704,-15.977013711578548,0.058116748371023715,3.1493969468978316,0.08137696155511805,1.9476736781417643 +57,36,7.12867616178041,0.06192372971384759,5.906390981561147,0.06256647853396405,1.2222851802192625,0.08802904371748357,3.052695537784646 +59,47,-5.098445862464769,0.05867877621198775,-7.56500667017755,0.059480106317872296,2.466560807712782,0.08355286844460776,-0.21963649550903788 +59,48,-8.782685210744836,0.057389958197961125,-10.555632606326496,0.05621626152777265,1.77294739558166,0.08033601534880018,0.10948733938328555 +63,64,2.7255540492069135,0.05412277888183962,2.123036967305174,0.05478313297127285,0.602517081901739,0.07700952442419487,-0.8659862151145178 +62,44,78.33004542493426,0.06047763186485523,77.5868371125521,0.060187212418090046,0.7432083123821551,0.0853231767730272,-2.270954603503167 +59,58,-3.708437136934966,0.07255513654970903,-3.5504151146381546,0.07244562364447284,-0.15802202229681106,0.1025310500530621,-1.0243059174093514 +65,58,8.025758060522941,0.057219675793214214,8.10403812586093,0.057402505368437655,-0.07828006533798947,0.08105022467861554,0.3569461967670842 +65,62,-81.65073144508942,0.05320694913275538,-81.42225325144494,0.05310051348031633,-0.2284781936444749,0.07517076538049133,1.807314544580463 +65,67,-14.27887379373184,0.045252906214721444,-12.949311690126544,0.04275038595505116,-1.3295621036052947,0.06225287961359064,-0.7604337869341908 +65,63,-2.8957682887914853,0.05486522021495164,-3.20390154212587,0.05413695700144576,0.30813325333438457,0.07707789892447461,0.9320122758327484 +65,68,-1.31294355039311,0.047647983308395835,-0.817472357268426,0.04695748158341655,-0.4954711931246839,0.06689794757699276,-0.29213414471068827 +67,68,13.014900975817243,0.04071366521489024,12.16109189516098,0.04127806233233603,0.8538090806562617,0.05797828011542238,0.46829964222350257 +65,70,1.9244881949455954,0.05453402576950175,3.525263564920512,0.056288108138350064,-1.6007753699749165,0.0783728976395748,-0.8211130426480319 +67,44,10.699055256729952,0.059308803980087185,8.958045925683544,0.05828619022678157,1.7410093310464085,0.08315536182773167,0.29679372801148673 +69,68,-3.974233912887045,0.053324634474670576,-5.550679439152973,0.053548322786346796,1.5764455262659283,0.07557075833341897,0.9422088217635535 +69,64,-3.3422188022646044,0.06169330104746012,-6.127636921295754,0.062271047000980545,2.7854181190311498,0.08765698311447225,1.3003690271924724 +69,60,9.882082869636294,0.07402939301641608,7.308191693967423,0.07212300481965171,2.5738911756688716,0.10335414290000425,2.586852149599585 diff --git a/summaries/dec_08_2025/merck/pfkfb3/dg_plot.png b/summaries/dec_08_2025/merck/pfkfb3/dg_plot.png new file mode 100644 index 0000000..4bb9d6d Binary files /dev/null and b/summaries/dec_08_2025/merck/pfkfb3/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/pfkfb3/dg_results.csv b/summaries/dec_08_2025/merck/pfkfb3/dg_results.csv new file mode 100644 index 0000000..0bc69a7 --- /dev/null +++ b/summaries/dec_08_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,-5.850568761947173,0.08448461561689698,-7.597684371217873 +23,Cn1ccc2ccc(-c3cc(Nc4cccnc4)cc4nccnc34)cc21,-6.555475770453476,0.08343358616513646,-7.963619986639076 +20,COc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-9.518277436352802,0.07198479068603603,-8.569347907703273 +42,CSc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-9.47956801878401,0.07705821745350894,-8.519388644068506 +24,Cn1ccc2ccc(-c3cc(Nc4ccccc4C#N)cc4nccnc34)cc21,-7.688392616877262,0.07515102223449452,-8.924999745202046 +33,Cn1ccc2ccc(-c3cc(Nc4cnccc4C#N)cc4nccnc34)cc21,-8.895089549465125,0.07327121129900459,-8.66037920468846 +26,Cn1ccc2ccc(-c3cc(Nc4ccccc4C(N)=O)cc4nccnc34)cc21,-7.488723929027945,0.06838435769954194,-9.226389986052087 +44,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(Br)cc2)c2nccnc2c1,-8.9996481305031,0.058171856550013876,-10.01046495048535 +34,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(N)=O)cc4nccnc34)cc21,-9.437880747359252,0.07423185299941197,-10.034314721268096 +29,Cn1ccc2ccc(-c3cc(Nc4ccccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.334295559616372,0.054225805462826716,-9.70592871414551 +35,Cn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-10.036108506492376,0.04719967864166907,-10.201778825003053 +57,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ccn(C(F)F)c3c2)c2nccnc2c1,-10.119309906505611,0.07271443184358149,-10.539443848422694 +37,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(=O)NC4CCOCC4)cc4nccnc34)cc21,-9.854218674094293,0.07294026645494558,-10.05915851439343 +30,COc1ncccc1Nc1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1,-6.154622413708634,0.08453063356679337,-9.255320097830385 +60,CC1(C)COc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.324964040756559,0.07111494818398242,-8.194315708437303 +31,COc1ccncc1Nc1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1,-9.448199432587767,0.05741647213205137,-9.340125266052516 +36,CN(c1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1)c1cnccc1S(C)(=O)=O,-9.159392565382314,0.0629726417676124,-7.486748310638047 +53,CCCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.265875592457025,0.06641386625242285,-7.041098038324923 +38,CN(C)c1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-8.989112663668937,0.05879138938453345,-8.813160062225876 +69,Cc1csc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-11.36193144944899,0.04833830283297837,-10.781167858036888 +41,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(OC(F)(F)F)c2)c2nccnc2c1,-9.93800660640459,0.07608991966378605,-7.43357666688315 +70,Cc1coc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-11.334628819245363,0.053506904605360096,-10.367937934210678 +43,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(Br)c2)c2nccnc2c1,-9.755710989689724,0.06056670319654542,-8.047337448876245 +39,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(N)c2)c2nccnc2c1,-7.048534356725749,0.06781975874227274,-7.242205016653798 +46,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(C(F)(F)F)cc2)c2nccnc2c1,-7.47436067443461,0.07105991680656752,-7.908173068126793 +49,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(N)cc2)c2nccnc2c1,-6.848925001489542,0.07642828449318056,-7.983570733571719 +62,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nonc3c2)c2nccnc2c1,-9.939677986312885,0.06366165779014302,-7.739510346982183 +63,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nsnc3c2)c2nccnc2c1,-9.11006836959391,0.06091589629623667,-8.614812615729898 +48,COc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-7.404012300162605,0.06722622792651908,-8.056085438002924 +47,CCc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.678196066325454,0.07325118758253032,-8.385209272895247 +52,CCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.500622971224953,0.06467722867303764,-10.459837137539063 +64,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ncsc3c2)c2nccnc2c1,-8.532262552814965,0.06313133229817355,-9.480798830844416 +54,CC(C)n1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.375986079537334,0.07185049007005231,-8.230388525015318 +55,Cn1ccc2c(F)cc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-11.06374672418159,0.0519668211381889,-10.701561147153257 +56,Cc1cc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc2c1ccn2C,-10.82305523752658,0.06186808880535503,-10.631343051751081 +58,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)CCO3)c2nccnc2c1,-9.810092095131068,0.07212249016636103,-9.189878694795562 +59,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)OCCO3)c2nccnc2c1,-9.280137975799956,0.07126537170420466,-8.16557277738621 +65,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3scnc3c2)c2nccnc2c1,-9.579494468568274,0.04547129336650976,-9.546824891562647 +67,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)nc3c2)c2nccnc2c1,-10.834607322769287,0.05428800048208335,-10.307258678496837 +68,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)cc3c2)c2nccnc2c1,-9.961893710158288,0.04815080480224423,-9.838959036273334 diff --git a/summaries/dec_08_2025/merck/shp2/README.md b/summaries/dec_08_2025/merck/shp2/README.md new file mode 100644 index 0000000..e0ba745 --- /dev/null +++ b/summaries/dec_08_2025/merck/shp2/README.md @@ -0,0 +1,38 @@ +# Shp2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.43 +- RMSE: 1.83 +- R²: 0.28 +- Kendall 𝜏: 0.42 +- Spearman ρ: 0.58 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 17.36 Hours +- Total Nanoseconds Simulated: 5627.60 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/shp2/ddg_results.csv b/summaries/dec_08_2025/merck/shp2/ddg_results.csv new file mode 100644 index 0000000..2aa4191 --- /dev/null +++ b/summaries/dec_08_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,-9.590117247846337,0.0592576445527005,-8.877190407073037,0.059719985599749614,-0.7129268407732993,0.08413052429391188,-1.5959089907842374 +11,Example 23,-7.173987192699012,0.06461122741598323,-5.570194209277854,0.06504335158246344,-1.6037929834211582,0.09168014121542273,-2.401074976228418 +4,Example 27,66.16922376565653,0.06707555558626412,66.05957429019732,0.06711656803922444,0.10964947545920743,0.09488816502899533,-2.7132072151203728 +3,6,-15.48767503410433,0.07582014889869992,-15.244702855300822,0.0740891932689205,-0.24297217880350705,0.10600897857380044,-2.583036201887811 +4,6,-14.642845339463555,0.08043078115279177,-14.363730233871745,0.07883284052201811,-0.2791151055918111,0.11262205512961583,-2.2216793949029503 +4,Example 14,45.66678951111179,0.09174040873872814,51.27075342674601,0.08943064937045628,-5.603963915634221,0.12811769449365845,-3.980730198782025 +7,6,-25.759133921112145,0.06833020652730472,-24.988392646746895,0.0654748050842598,-0.7707412743652483,0.09463597215058304,-0.9594901697802434 +Example 14,3,-44.67577492674166,0.08905910102583688,-50.385231584650796,0.08556444729460631,5.709456657909136,0.12350221907464529,4.342087005766886 +Example 14,Example 27,22.194153953322132,0.08179958773164077,14.736727368510289,0.07942828756709273,7.457426584811842,0.1140176539791412,1.2675229836616524 +Example 1,7,20.073603026585573,0.07302631885838233,18.781664996888207,0.07238535456357544,1.291938029697366,0.10282257923870933,1.9235839513310684 +Example 1,Example 3,-11.938976535589537,0.06987150107826695,-10.34106055678972,0.06801380214704615,-1.597915978799818,0.09750848140253134,0.7771021976732414 +Example 1,Example 5,3.271016280909115,0.04996444835246129,2.1551495526669724,0.04748472306568153,1.1158667282421424,0.06892927552056702,1.4339357903539591 +Example 1,Example 4,-11.92776354233886,0.06922117166966867,-10.751743123442116,0.06537686025322512,-1.1760204188967442,0.09521399300466013,0.7919761025218072 +Example 22,10,9.85435617684526,0.06611046790326752,10.053741677167327,0.06305508966143142,-0.1993855003220679,0.09135939086158641,2.0975000377510162 +Example 22,Example 1,-66.89107930960293,0.05033217389574902,-68.77799366162238,0.05024527008981794,1.8869143520194418,0.07111901922461158,0.2522139828111576 +Example 22,11,7.819938942991651,0.06946894495885707,6.83451233218717,0.0720498577646265,0.9854266108044808,0.10008554499826447,2.9026660231951964 +Example 22,Example 24,1.116870874561033,0.041586771632592244,0.38098318787228275,0.04401657484899338,0.7358876866887502,0.060555085965246676,0.16262102901980635 +Example 22,Example 25,1.835129017454525,0.04953418446377944,0.4105955471694231,0.048413550038209976,1.424533470285102,0.06926404014922888,0.37121625155419696 +Example 22,Example 26,0.09180054796664376,0.05441249887539159,0.3187604606268424,0.051206690046542915,-0.2269599126601986,0.07471843908559123,0.2815209870088881 +Example 24,Example 25,-0.10709112273297493,0.05423016504936695,0.22412665143631827,0.0556989527443555,-0.3312177741692932,0.07773856274783789,0.2085952225343906 +Example 26,Example 24,2.5196520749700815,0.05523752621793533,2.1790160924513837,0.054208588922840695,0.3406359825186976,0.07739351016514641,-0.11889995798908173 +Example 22,Example 28,-0.21175949694475857,0.08159248359513488,0.6842624831132774,0.08158989782945512,-0.8960219800580359,0.11538736848998368,0.7863357641631342 +Example 22,Example 9,-13.515338696218734,0.0760002721573115,-8.486229898843286,0.07610872272572129,-5.02910879737545,0.1075573290990723,0.4475017016926592 +Example 22,Example 29,1.731108568405594,0.0809575333511539,1.8559285267336247,0.0793631583591183,-0.12481995832803074,0.11336945404754176,1.6260883163945343 +Example 26,Example 25,1.8666556181280851,0.06209155021245766,0.682674015222369,0.06155519552569948,1.183981602905716,0.08743227495606667,0.08969526454530886 +Example 2,Example 30,33.65166555423238,0.044485829007808654,36.81019845914158,0.043502441633516145,-3.1585329049092032,0.062220988505402815,-0.886345539506191 +Example 2,Example 6,-9.908330367902021,0.0477262045346528,-8.279671260689472,0.044808963083046174,-1.628659107212549,0.06546475213319997,-0.7979687379277243 +Example 28,Example 23,0.1849482794046634,0.08185629756891186,0.2160528949252693,0.07968278109316068,-0.031104615520605894,0.1142357170697099,-0.28474471719635547 +Example 29,Example 23,-1.0852361948576583,0.08125586455344692,-0.8540640583186532,0.07978090961757445,-0.2311721365390052,0.11387497119093246,-1.1244972694277557 +Example 2,Example 4,-14.576595488251485,0.07089276890601741,-12.845291470816669,0.06979171704450464,-1.7313040174348147,0.09948200063922212,0.07559798666580186 +Example 4,Example 3,0.07811176737110048,0.03554806042930046,0.2909778649079379,0.03428173258341767,-0.2128660975368374,0.04938523857597691,-0.014873904848565751 +Example 30,Example 5,-33.454036806626014,0.05643513073571964,-36.841718323508374,0.05209393274159172,3.3876815168823637,0.07680300651434975,1.6039032140041447 +Example 30,Example 3,-49.70681699211434,0.07242207716507681,-49.27866632392458,0.06913572138952968,-0.42815066818975567,0.10012344996530538,0.9470696213234271 +Example 6,6,-0.42553433693336146,0.06069338145099894,0.3076358440808567,0.056397049083340395,-0.7331701810142182,0.08285115386803715,1.0456844036225441 +Example 6,Example 5,9.938042316749785,0.0595960819669513,7.628018614764568,0.056390057602120625,2.310023701985217,0.08204591142879734,1.515526412425678 +Example 6,7,24.458592198435987,0.0769105199901519,25.242338673448987,0.07285239948148844,-0.7837464750129977,0.10593724649699901,2.0051745734027873 +Example 9,Example 8,4.80657916988709,0.05076636866033812,4.503069738823045,0.05143806747041423,0.30350943106404504,0.07227101059241006,-0.9239359369425386 +Example 8,Example 23,9.129658127320402,0.07042406809817539,5.476102625485344,0.06799922230240812,3.6535555018350574,0.09789506423323274,0.9780252822166582 +SHP099-1/Example 7,10,14.902026903888363,0.04333621118069348,13.877208934606887,0.04551806200704333,1.0248179692814765,0.0628483982960163,2.614505349709493 +Example 9,6,-57.319089396342385,0.06344597536916935,-64.99370860791082,0.06499520325450449,7.6746192115684355,0.09082823479865494,0.7688060626693235 +SHP099-1/Example 7,11,13.29271340443437,0.05529220227582494,10.66274351392639,0.05625406955955956,2.6299698905079802,0.0788780576239204,3.419671335153674 +SHP099-1/Example 7,Example 30,-25.8593571974572,0.04070598241505221,-25.368609378302327,0.04100988227181026,-0.4907478191548711,0.057782241634625746,0.599251871119449 +SHP099-1/Example 7,Example 28,4.753433936489175,0.07479937654364095,4.5345032988232585,0.07295941117728692,0.2189306376659173,0.10448934113417409,1.3033410761216113 +SHP836-2,Example 27,65.28067430698795,0.04315878186680905,66.4059664256764,0.045492733016707254,-1.1252921186884501,0.06270780820245764,-1.8165292720657737 +SHP099-1/Example 7,Example 29,6.385177587196305,0.07324846157621276,5.882935396547823,0.07225354677287292,0.5022421906484819,0.10288786198838837,2.1430936283530118 +SHP099-1/Example 7,Example 8,-4.441940511622331,0.058654407181624735,-0.6961584978855538,0.05906429847861952,-3.745782013736777,0.08324019964295669,0.0405710767085977 +SHP836-2,3,-0.205759428177944,0.05401293787433902,1.0961340233074086,0.05401484319713036,-1.3018934514853526,0.07638717656405286,1.2580347500394595 +SHP836-2,6,-15.678368099781123,0.06920472519428417,-14.140952035240995,0.06765824461258713,-1.5374160645401282,0.09678291199004636,-1.3250014518483515 diff --git a/summaries/dec_08_2025/merck/shp2/dg_plot.png b/summaries/dec_08_2025/merck/shp2/dg_plot.png new file mode 100644 index 0000000..e38883c Binary files /dev/null and b/summaries/dec_08_2025/merck/shp2/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/shp2/dg_results.csv b/summaries/dec_08_2025/merck/shp2/dg_results.csv new file mode 100644 index 0000000..12c9c73 --- /dev/null +++ b/summaries/dec_08_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,-8.35735182317549,0.061515241367126126,-7.198715959005226 +Example 23,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Cl)CC1,-9.078959928116662,0.05502477469982573,-8.794624949789464 +11,CNc1nc(N2CCC(C)([NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-7.108437343206692,0.06302882838424184,-6.393549973561046 +4,C[C@@H]1CN(c2ncc(-c3ccc(Cl)c(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-6.937852872531455,0.0923211683764137,-5.85822883749131 +Example 27,C[C@@H]1CN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-6.536207563862365,0.09142971020624134,-8.571436052611682 +3,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-6.983394084622709,0.09395266847978412,-5.496872030506449 +6,Nc1nc(N2CCC([NH3+])CC2)ncc1-c1cccc(Cl)c1Cl,-7.166432413766619,0.05420511783059981,-8.07990823239426 +Example 14,Nc1nc(N2CC[C@@H](C[NH3+])C2)cnc1-c1cccc(Cl)c1Cl,-13.139532941891542,0.10047328157269529,-9.838959036273334 +7,C[NH+](C)C1CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-6.582599560681291,0.05272756826305389,-7.120418062614016 +Example 1,CC1([NH3+])CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-6.901330661152239,0.050866493158928286,-9.044002013945084 +Example 3,CC1([NH3+])CCN(c2ncc(-c3ccc(Cl)s3)c(N)n2)CC1,-8.627951035225015,0.07043724549897153,-8.266899816271843 +Example 5,COc1cc(Cl)c(Cl)c(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1,-5.484707109877726,0.053468264740141276,-7.610066223591126 +Example 4,Cc1ccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)s1,-8.219977639571981,0.06396779250221933,-8.252025911423278 +Example 22,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Br)CC1,-8.494787776868058,0.04371842239894173,-9.296215996756242 +Example 24,Cc1nc(-c2cccc(Cl)c2Cl)c(N)nc1N1CCC(C)([NH3+])CC1,-7.671514565449931,0.06250114218744622,-9.133594967736435 +Example 25,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C#N)CC1,-7.424708300325265,0.07424344187544399,-8.924999745202046 +Example 26,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C(N)=O)CC1,-8.442314166924556,0.0629506465462494,-9.014695009747355 +Example 28,CC1([NH3+])CCN(c2cnc(-c3cccc4cc[nH]c34)c(N)n2)CC1,-9.13532313531196,0.08050823813947773,-8.509880232593108 +Example 9,Nc1nc(N2CCC(C[NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-13.908281987512924,0.054499098285608796,-8.848714295063584 +Example 29,CC1([NH3+])CCN(c2cnc(C3=CCCCC3)c(N)n2)CC1,-8.726559493506171,0.0661283025325899,-7.670127680361708 +Example 2,Cc1cccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1Cl,-5.852659549796628,0.0432486121723713,-8.32762389808908 +Example 30,CC1([NH3+])CCN(c2nnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.137456981195317,0.04290404614840922,-9.21396943759527 +Example 6,CC1([NH3+])CCN(c2ncc(-c3cc(O)cc(Cl)c3Cl)c(N)n2)CC1,-7.066127599489822,0.048055289346077654,-9.125592636016805 +Example 8,CC1(C[NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-13.187763011718445,0.06222958009918763,-9.772650232006121 +SHP099-1/Example 7,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.217927520968107,0.044202561659043564,-9.81322130871472 +SHP836-2,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-5.541740253157531,0.0879235334463859,-6.754906780545908 diff --git a/summaries/dec_08_2025/merck/syk_negative/README.md b/summaries/dec_08_2025/merck/syk_negative/README.md new file mode 100644 index 0000000..8c44d61 --- /dev/null +++ b/summaries/dec_08_2025/merck/syk_negative/README.md @@ -0,0 +1,38 @@ +# Syk Negative Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.73 +- RMSE: 0.84 +- R²: 0.63 +- Kendall 𝜏: -0.07 +- Spearman ρ: -0.03 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.40 Hours +- Total Nanoseconds Simulated: 1673.60 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/syk_negative/ddg_results.csv b/summaries/dec_08_2025/merck/syk_negative/ddg_results.csv new file mode 100644 index 0000000..2cb0fa0 --- /dev/null +++ b/summaries/dec_08_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) +CHEMBL3264995,CHEMBL3265001,17.951197649546096,0.05845138784941532,17.5048950433902,0.0582287947535127,0.44630260615589545,0.0825054984832495,0.34566735513927593 +CHEMBL3264995,CHEMBL3265000,-11.09477012216787,0.06258587846851879,-10.396566098141868,0.06306729822690085,-0.6982040240260005,0.0888508654393251,0.5739938399963156 +CHEMBL3264997,CHEMBL3264998,0.914795728808002,0.07232636108838066,0.7198790110314608,0.07012031016403793,0.19491671777654124,0.10073708555337356,-0.7336044857199532 +CHEMBL3264994,CHEMBL3264995,-5.851426614519463,0.08254849698066899,-2.5621953763798007,0.08117069454264672,-3.2892312381396622,0.11577104994904026,-2.5925659381562567 +CHEMBL3264994,CHEMBL3265001,7.592515045360938,0.08646870328485962,11.124851118992172,0.08275087342638766,-3.532336073631234,0.11968518580256757,-2.2468985830169808 +CHEMBL3264997,CHEMBL3264994,6.173570098482263,0.08402903979493233,2.708240696615127,0.08408138930801866,3.4653294018671357,0.11887203017036815,1.1853758538405335 +CHEMBL3264997,CHEMBL3265001,14.876303796237421,0.07151722776260079,13.974369342996203,0.0701391585149042,0.9019344532412175,0.1001709310330426,-1.061522729176447 +CHEMBL3264998,CHEMBL3265000,-13.168057013228267,0.07336968709484022,-13.117964985458869,0.07286377719299393,-0.050092027769398834,0.10340329303859247,-0.09959175859945434 +CHEMBL3264998,CHEMBL3265001,17.605267477505812,0.06874683073005994,17.288275651768856,0.06718032670920303,0.31699182573695667,0.09612139736907059,-0.32791824345649395 +CHEMBL3265001,CHEMBL3265000,-29.119019545591094,0.07587465784191008,-28.684858497694623,0.07338778113462696,-0.43416104789646925,0.10555913092902401,0.22832648485703963 diff --git a/summaries/dec_08_2025/merck/syk_negative/dg_plot.png b/summaries/dec_08_2025/merck/syk_negative/dg_plot.png new file mode 100644 index 0000000..fc273fc Binary files /dev/null and b/summaries/dec_08_2025/merck/syk_negative/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/syk_negative/dg_results.csv b/summaries/dec_08_2025/merck/syk_negative/dg_results.csv new file mode 100644 index 0000000..67b68a2 --- /dev/null +++ b/summaries/dec_08_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) +CHEMBL3264995,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-11.924951283562377,0.039294514533548555,-12.458424187983185 +CHEMBL3265001,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5nnn[n-]5)cc4)c3)cn3ccnc23)cc1OC,-11.72454186740713,0.03794940339965723,-12.112756832843909 +CHEMBL3265000,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(=O)[N-]S(C)(=O)=O)cc4)c3)cn3ccnc23)cc1OC,-12.3685821666144,0.04860528620500494,-11.88443034798687 +CHEMBL3264997,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4cccc(C(=O)[O-])c4)c3)cn3ccnc23)cc1OC,-12.38060179843907,0.05089504447317084,-11.051234103667463 +CHEMBL3264998,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(CC(=O)[O-])cc4)c3)cn3ccnc23)cc1OC,-12.175091540800352,0.051079286976282855,-11.784838589387416 +CHEMBL3264994,CC(C)(C)c1ccc(Nc2nc(-c3cccc(NC(=O)c4ccc(C(=O)[O-])cc4)c3)cn3ccnc23)cc1,-8.583773654872443,0.059095429715499866,-9.865858249826928 diff --git a/summaries/dec_08_2025/merck/syk_neutral/README.md b/summaries/dec_08_2025/merck/syk_neutral/README.md new file mode 100644 index 0000000..ed08870 --- /dev/null +++ b/summaries/dec_08_2025/merck/syk_neutral/README.md @@ -0,0 +1,38 @@ +# Syk Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.30 +- RMSE: 1.58 +- R²: 0.01 +- Kendall 𝜏: -0.01 +- Spearman ρ: -0.03 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 17.59 Hours +- Total Nanoseconds Simulated: 7729.00 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/syk_neutral/ddg_results.csv b/summaries/dec_08_2025/merck/syk_neutral/ddg_results.csv new file mode 100644 index 0000000..7a6ea0c --- /dev/null +++ b/summaries/dec_08_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,CHEMBL3265019,6.978170976109875,0.06251039754881196,7.960593664324686,0.06297362984547286,-0.9824226882148108,0.08873121129357553,-0.20261722132296622 +CHEMBL3264999,CHEMBL3265004,19.9064760562085,0.059720210843642464,20.620496502522464,0.06137319540365401,-0.7140204463139628,0.08563394594005469,0.5599657866115306 +CHEMBL3264999,CHEMBL3265002,16.079737459544013,0.06377585906156442,16.592609886110257,0.06301268652257865,-0.5128724265662452,0.08965466447337413,0.8016897962257247 +CHEMBL3264996,CHEMBL3265003,6.4026074304773655,0.06585966319832731,8.355355125188026,0.06437946125840488,-1.9527476947106612,0.0920989156750478,-0.15602024454645136 +CHEMBL3264999,CHEMBL3265006,-3.866358044736597,0.07805562711386639,-6.768403226884336,0.07521202685682069,2.9020451821477393,0.10839524854923333,1.4650152881562122 +CHEMBL3264996,CHEMBL3265006,-15.360393719323849,0.07793820715021481,-18.138647678006627,0.0759541874500186,2.7782539586827784,0.10882739877890289,0.7122497251244222 +CHEMBL3265002,CHEMBL3264996,-6.0640808069503125,0.06363086185709532,-6.876785015275183,0.0625462518842128,0.8127042083248706,0.08922398895723135,-0.04892423319393453 +CHEMBL3265002,CHEMBL3265003,0.09555561852750082,0.04728587763550691,1.8840625531536785,0.04763866865967342,-1.7885069346261777,0.06712225395072996,-0.20494447774038588 +CHEMBL3265002,CHEMBL3265004,4.444596668954842,0.048775623047545846,4.189736822995284,0.04887231068378528,0.25485984595955863,0.06904754995833465,-0.24172400961419407 +CHEMBL3265003,CHEMBL3265004,3.668655363229631,0.04789144726547641,2.2359059541322224,0.04903922272571469,1.4327494090974087,0.06854513904518802,-0.036779531873808176 +CHEMBL3264999,CHEMBL3265008,-2.9955117480676923,0.07243095720223479,-5.339944625097285,0.06852527083620921,2.344432877029593,0.0997093591615541,1.639778132435602 +CHEMBL3265008,CHEMBL3265005,-1.1743239042155702,0.04737328715580209,-1.2511114908036414,0.046513579479365345,0.07678758658807117,0.06639082325087799,-0.5422872709712577 +CHEMBL3265008,CHEMBL3265009,6.379944087512898,0.03817018655511429,6.726712928936759,0.03681047565941696,-0.3467688414238601,0.05302805163236488,-0.5164565984060626 +CHEMBL3265008,CHEMBL3265006,5.699873838008239,0.05954185947324383,6.126463647506217,0.05605657978613148,-0.4265898094979777,0.08177758352293396,-0.17476284427938982 +CHEMBL3265006,CHEMBL3265011,2.3013221775902855,0.06640484138564888,-0.8155209894676135,0.06312454236005176,3.116843167057899,0.09162047155313684,1.3283567995406866 +CHEMBL3265008,CHEMBL3265011,7.73494511398372,0.057608910906811715,5.070739133056368,0.05464792457066852,2.6642059809273517,0.07940517789004976,1.1535939552612968 +CHEMBL3265012,CHEMBL3259820,-0.13026880158044646,0.03891230846083164,-0.6548875771709045,0.03868075521142255,0.5246187755904581,0.05486682580099657,-0.029567948602893968 +CHEMBL3265012,CHEMBL3265013,8.302184756786671,0.038388710330283224,7.0557751044691335,0.03653313022489471,1.2464096523175385,0.05299398725187141,0.737624395793219 +CHEMBL3265008,CHEMBL3265022,18.984551701717997,0.06357524026420097,18.5009622366389,0.06383485427214271,0.4835894650790947,0.0900927288664106,-1.0132183634783043 +CHEMBL3265009,CHEMBL3265011,0.5129655249375112,0.06120976997142682,-1.7905417539299378,0.06032842409325718,2.303507278867449,0.08594274078437851,1.6700505536673593 +CHEMBL3265013,CHEMBL3259820,-7.941968790349016,0.05064453172832437,-7.20554992078852,0.04949535144863797,-0.7364188695604965,0.07081425286625175,-0.767192344396113 +CHEMBL3265012,CHEMBL3265025,15.601069166251301,0.06497244637684892,15.453484096782455,0.06115385863385114,0.14758506946884653,0.08922563092520869,0.34899146493264793 +CHEMBL3265014,CHEMBL3265010,-2.0779226756209535,0.06150278090640674,-1.7017062374064718,0.058494128960845104,-0.3762164382144814,0.08487729485621845,0.2694576036564737 +CHEMBL3265014,CHEMBL3265015,1.090765214452234,0.06430483029662244,-0.5315483860835143,0.06001136809778969,1.6223136005357481,0.08795723677131871,0.928647183772851 +CHEMBL3265016,CHEMBL3265017,-2.483343067661869,0.036673058262094216,-1.44407930529158,0.0368249446626064,-1.039263762370289,0.051971047244585906,0.20373888630455644 +CHEMBL3265014,CHEMBL3265023,10.657833028371158,0.06730580710259566,11.69336362058149,0.06864670533181422,-1.0355305922103322,0.09613761918544035,-0.07746351590252384 +CHEMBL3265015,CHEMBL3259820,-7.474575926245968,0.06077880754280338,-6.520348809029816,0.05854873780571055,-0.9542271172161517,0.08439205024744317,-1.105184054101423 +CHEMBL3265016,CHEMBL3265021,-4.6002332961005665,0.04169784704419217,-3.1803644625970544,0.04311869307546409,-1.4198688335035123,0.05998276536353522,0.8039603940083501 +CHEMBL3265018,CHEMBL3265019,0.3189913404321323,0.0367072862319063,0.8896253807253477,0.037259565696349785,-0.5706340402932154,0.052303920487777045,0.4132299238262116 +CHEMBL3265015,CHEMBL3265023,8.87023215683181,0.0720881559488641,11.507896996656724,0.0703990266258289,-2.6376648398249154,0.10076073232153446,-1.0061106996753748 +CHEMBL3265020,CHEMBL3265017,-1.351590937575715,0.04178036278098102,-1.0803792003374109,0.04271301924490991,-0.27121173723830405,0.05974948306995156,-0.486924208446843 +CHEMBL3265020,CHEMBL3265021,-3.696638088795907,0.03867342768982572,-2.5356629924451464,0.036627605050637446,-1.1609750963507606,0.05326551849954773,0.11329729925695062 +CHEMBL3265016,CHEMBL3265025,1.0911331324424145,0.07176274298468217,2.839207895065211,0.07091200408227885,-1.7480747626227966,0.10088807463546265,1.4995356858393165 +CHEMBL3265018,CHEMBL3265017,7.4080771413873165,0.07198672000481414,6.2082601684634495,0.07100797119868224,1.1998169729238668,0.10111488431880043,-0.3013902408500404 +CHEMBL3265018,CHEMBL3265021,5.02721380234041,0.07243967451037854,4.75237205825385,0.07357946397871308,0.2748417440865598,0.10325426849561388,0.29883126685375316 +CHEMBL3265019,CHEMBL3265017,7.4390625796798835,0.0705027135250764,5.126359091396036,0.07119893319628004,2.3127034882838466,0.10019940470226027,-0.714620164676252 +CHEMBL3265020,CHEMBL3265025,1.4080866793208018,0.07028733548384224,3.1260890205977634,0.06919344641385386,-1.7180023412769616,0.09863083978170852,0.8088725910879172 +CHEMBL3265022,CHEMBL3265017,-2.9675381361162323,0.053106175018908464,-2.7853036021707522,0.050822327131180456,-0.18223453394548017,0.073506290616298,-0.7002540535779291 +CHEMBL3265022,CHEMBL3265009,-10.820431243915982,0.06859267592729298,-11.379286061991964,0.06967458458043013,0.5588548180759824,0.09777271054502966,0.4967617650722418 +CHEMBL3265022,CHEMBL3265010,-15.796313753676069,0.06886930433542651,-14.884375445519582,0.06819042489270963,-0.9119383081564846,0.09691705281679727,0.6629778064063347 +CHEMBL3265023,CHEMBL3265010,-10.594261225653481,0.06362521319042747,-10.731469954895456,0.06284588875219935,0.1372087292419741,0.0894302716454622,0.3469211195589975 +CHEMBL3265023,CHEMBL3265021,-2.7097837600989347,0.052154586120746076,-2.9745441259273875,0.05158419222564893,0.26476036582845297,0.0733555024589091,-0.4160892327214727 +CHEMBL3265024,CHEMBL3265005,-15.625999867014151,0.06543342659916844,-17.26543907243575,0.0629505543303148,1.6394392054216,0.09079815861019803,1.4705146701861602 +CHEMBL3265026,CHEMBL3265024,-12.103600857127502,0.04533318379379568,-10.64331475025359,0.045911443841833106,-1.4602861068739121,0.06452099060401857,-0.42605116554008615 +CHEMBL3265024,CHEMBL3265013,-8.70657536608119,0.06726445461072578,-9.10114495674149,0.06639153210024008,0.394569590660301,0.09451107019125114,1.9837592544965157 +CHEMBL3265026,CHEMBL3265025,-13.035505686866895,0.051102262219218944,-10.92309021897623,0.050948590670653,-2.112415467890666,0.07216093191781521,1.1690751580958585 +CHEMBL3265026,CHEMBL3265005,-29.767692813989104,0.06623944455176348,-28.499454125225725,0.06350255329211078,-1.2682386887633776,0.09176185639547359,1.044463504646074 +CHEMBL3265027,CHEMBL3265028,0.5913626082954405,0.05040226087724252,1.98896666130628,0.04873859288792739,-1.3976040530108393,0.07011303971610942,-0.6845972934356985 +CHEMBL3265027,CHEMBL3265029,0.8857374597156618,0.04839600007310999,1.5126696498144674,0.04841262119129259,-0.6269321900988057,0.06845403358231021,-0.8003462675468339 +CHEMBL3265028,CHEMBL3265017,7.258241249567258,0.05049489302464047,7.203517270695472,0.05001301299794364,0.054723978871785615,0.07107063873852806,-0.4799514416868219 +CHEMBL3265027,CHEMBL3265030_n,14.776286661676028,0.05647473527863458,15.450513722169275,0.05752551318716368,-0.6742270604932464,0.08061377296863356,-1.1490630654569578 +CHEMBL3265028,CHEMBL3265021,4.339041310251061,0.05437358677993489,5.600563521335435,0.05487332254651281,-1.2615222110843727,0.07725003861881716,0.12027006601697166 +CHEMBL3265029,CHEMBL3265035,5.7207137120797595,0.05812171669792992,6.2805118137296265,0.05827520207647073,-0.5597981016498669,0.08230512213081227,0.049027456250526714 +CHEMBL3265031,CHEMBL3265037,7.115550133604594,0.058845257370957395,7.937410372591086,0.06069036783128416,-0.8218602389864917,0.08453451994629642,-0.6900325661237705 +CHEMBL3265029,CHEMBL3265030_n,53.908558528628724,0.07203657420956067,54.61117517003837,0.07311707772158749,-0.7026166414096486,0.10264197522648424,-0.3487167979101238 +CHEMBL3265032,CHEMBL3265031,1.877015983362812,0.047988576617929345,1.9274799147780528,0.05026814605824408,-0.05046393141524083,0.06949669052514541,-1.016310740425268 +CHEMBL3265033,CHEMBL3265031,45.8999936397115,0.04710558268339113,45.686178284392994,0.047115553829261976,0.21381535531850143,0.06662440493227599,-0.24172400961419407 +CHEMBL3265032,CHEMBL3265029,-23.852286570694243,0.06461869405928966,-24.165709933226406,0.06418154979954628,0.3134233625321609,0.09107605040074869,-0.05682057064502382 +CHEMBL3265033,CHEMBL3265032,45.184669426869114,0.05361373656452312,44.22819664640773,0.05368472456494165,0.9564727804613816,0.07587148608023789,0.7745867308110739 +CHEMBL3265034,CHEMBL3265029,-15.335663171930621,0.0681111729752891,-15.37450763640556,0.06900915917696189,0.038844464474939874,0.09696079586297245,0.3642024675756866 +CHEMBL3265034,CHEMBL3265021,-11.333618016107652,0.0753168123034587,-8.820842761003366,0.07510386615726926,-2.5127752551042866,0.10636358835298594,0.6002215077037936 +CHEMBL3265036,CHEMBL3265032,1.4023985571913178,0.06856028383286221,1.1192917333985686,0.06734670533713553,0.28310682379274915,0.09610458490108359,-0.654953933440404 +CHEMBL3265036,CHEMBL3265033,-45.278189475885455,0.06682139574101537,-44.388547306556674,0.0668155068118758,-0.8896421693287763,0.09449556010366418,-1.4295406642514779 +CHEMBL3265034,CHEMBL3265030_n,38.79267496286098,0.07847092242988321,39.22390483704469,0.07844137924668018,-0.4312298741837112,0.11095375453367164,0.01548566966556277 +CHEMBL3265036,CHEMBL3265035,-16.44495592556527,0.0674773717744375,-16.40246060132419,0.06627736865007765,-0.042495324241083474,0.09458269025970846,-0.662747047834901 +CHEMBL3265037,CHEMBL3265017,-26.870433941334657,0.06355451400267845,-27.56045763076742,0.06208230424186351,0.6900236894327638,0.08884474520249329,1.285320268328328 +CHEMBL3265037,CHEMBL3265035,-26.08212344449063,0.06787350672976447,-26.542263778291904,0.06731635639801233,0.46014033380127384,0.09559448077425599,1.6985501921545414 diff --git a/summaries/dec_08_2025/merck/syk_neutral/dg_plot.png b/summaries/dec_08_2025/merck/syk_neutral/dg_plot.png new file mode 100644 index 0000000..224e106 Binary files /dev/null and b/summaries/dec_08_2025/merck/syk_neutral/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/syk_neutral/dg_results.csv b/summaries/dec_08_2025/merck/syk_neutral/dg_results.csv new file mode 100644 index 0000000..971a2c7 --- /dev/null +++ b/summaries/dec_08_2025/merck/syk_neutral/dg_results.csv @@ -0,0 +1,39 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL3259820,COc1ccc(Nc2nc(-c3ccc(C(N)=O)cc3)cn3ccnc23)cc1OC,-11.104903411058274,0.05995043748302887,-10.64136286343957 +CHEMBL3265019,COc1ccc(Nc2nc(-c3ccc4nn[nH]c4c3)cn3ccnc23)cc1OC,-12.343424826643638,0.056037325091686026,-10.843980084762535 +CHEMBL3264999,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(C(N)=O)cc4)c3)cn3ccnc23)cc1OC,-13.072014316252616,0.08655278286798061,-11.484905964818156 +CHEMBL3265004,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5cn[nH]c5)cc4)c3)cn3ccnc23)cc1OC,-13.71670125090435,0.09737492584913522,-10.924940178206626 +CHEMBL3265002,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5ncc[nH]5)cc4)c3)cn3ccnc23)cc1OC,-13.76233308637602,0.09169678833100241,-10.683216168592432 +CHEMBL3264996,COC(=O)c1ccc(NC(=O)c2cccc(-c3cn4ccnc4c(Nc4ccc(OC)c(OC)c4)n3)c2)cc1,-13.199402138266507,0.10449612721438031,-10.732140401786365 +CHEMBL3265003,COc1ccc(Nc2nc(-c3cccc(C(=O)Nc4ccc(-c5ccn[nH]5)cc4)c3)cn3ccnc23)cc1OC,-15.311222270818005,0.0980289860397962,-10.888160646332818 +CHEMBL3265006,CNC(=O)c1cccc(-c2cn3ccnc3c(Nc3ccc(OC)c(OC)c3)n2)c1,-10.570626958106448,0.0803189266760173,-10.019890676661944 +CHEMBL3265008,COc1ccc(Nc2nc(-c3ccc(F)c(C(N)=O)c3)cn3ccnc23)cc1OC,-10.263081604303357,0.057311150474037675,-9.845127832382554 +CHEMBL3265005,COc1ccc(Nc2nc(-c3cccc(C(N)=O)c3)cn3ccnc23)cc1OC,-10.120423422617831,0.05692923951313482,-10.387415103353812 +CHEMBL3265009,COc1ccc(Nc2nc(-c3ccc(C)c(C(N)=O)c3)cn3ccnc23)cc1OC,-10.328087155706175,0.06702059065673895,-10.361584430788616 +CHEMBL3265011,COc1ccc(Nc2nc(-c3cc(C(N)=O)ccc3C)cn3ccnc23)cc1OC,-7.696550004964806,0.06999751182430033,-8.691533877121257 +CHEMBL3265012,COc1ccc(Nc2nc(-c3ccc(C(N)=O)c(F)c3)cn3ccnc23)cc1OC,-11.6774941256155,0.06256587258655529,-10.611794914836675 +CHEMBL3265013,COc1ccc(Nc2nc(-c3ccc(C(N)=O)c(C)c3)cn3ccnc23)cc1OC,-10.457169041836604,0.0570661860285642,-9.874170519043457 +CHEMBL3265022,COc1ccc(Nc2nc(-c3ccc4cnn(C)c4c3)cn3ccnc23)cc1OC,-10.353619411325562,0.049818672441404616,-10.85834619586086 +CHEMBL3265025,COc1ccc(Nc2nc(-c3ccc4c(c3)OCC(=O)N4)cn3ccnc23)cc1OC,-11.582830360528675,0.0490096520768984,-10.262803449904027 +CHEMBL3265014,COc1ccc(Nc2nc(-c3ccc(C(N)=O)c(OC)c3)cn3ccnc23)cc1OC,-11.113786236432547,0.07615788579141705,-10.464825993110997 +CHEMBL3265010,COc1ccc(Nc2nc(-c3ccc(OC)c(C(N)=O)c3)cn3ccnc23)cc1OC,-11.515044179610308,0.07118169396665684,-10.195368389454524 +CHEMBL3265015,COc1ccc(Nc2nc(-c3ccc(C(N)=O)cc3C)cn3ccnc23)cc1OC,-9.679566098234487,0.07411282703287876,-9.536178809338146 +CHEMBL3265016,COc1ccc(Nc2nc(-c3ccc4cc[nH]c4c3)cn3ccnc23)cc1OC,-9.695493726793872,0.050619035758119615,-11.762339135743344 +CHEMBL3265017,COc1ccc(Nc2nc(-c3ccc4cn[nH]c4c3)cn3ccnc23)cc1OC,-10.473086162178703,0.04107142545752853,-11.558600249438788 +CHEMBL3265023,COc1ccc(Nc2nc(-c3ccc4c(cnn4C)c3)cn3ccnc23)cc1OC,-11.892482936339308,0.06740789656253791,-10.542289509013521 +CHEMBL3265021,COc1ccc(Nc2nc(-c3ccc4[nH]ncc4c3)cn3ccnc23)cc1OC,-11.41470223763433,0.04784589813979768,-10.958378741734993 +CHEMBL3265018,COc1ccc(Nc2nc(-c3ccc4nc[nH]c4c3)cn3ccnc23)cc1OC,-11.741240511247812,0.060699623296479155,-11.257210008588746 +CHEMBL3265020,COc1ccc(Nc2nc(-c3ccc4[nH]ccc4c3)cn3ccnc23)cc1OC,-10.179612076406608,0.043650484036980845,-11.071676040991944 +CHEMBL3265024,COc1ccc(Nc2nc(-c3ccc4c(c3)NC(=O)CO4)cn3ccnc23)cc1OC,-11.092672743463359,0.05872997019047232,-11.857929773539972 +CHEMBL3265026,COc1ccc(Nc2nc(-c3ccc4c(c3)NCCO4)cn3ccnc23)cc1OC,-9.407777843583629,0.06026633813977186,-11.431878607999886 +CHEMBL3265027,c1ccc(Nc2nc(-c3ccc4cn[nH]c4c3)cn3ccnc23)cc1,-8.945972903271771,0.06678897756480161,-10.394051514316267 +CHEMBL3265028,COc1cccc(Nc2nc(-c3ccc4cn[nH]c4c3)cn3ccnc23)c1,-10.351607282851774,0.06052696327079611,-11.078648807751966 +CHEMBL3265029,COc1ccc(Nc2nc(-c3ccc4cn[nH]c4c3)cn3ccnc23)cc1,-9.443592986377174,0.0665043277597312,-11.1943977818631 +CHEMBL3265030_n,CC1(O)CN(c2ccc(Nc3nc(-c4ccc5cn[nH]c5c4)cn4ccnc34)cc2)C1,-9.788916879769147,0.08300995313080428,-11.543114579773224 +CHEMBL3265035,CN(CCO)c1ccc(Nc2nc(-c3ccc4cn[nH]c4c3)cn3ccnc23)cc1,-10.146246637736855,0.08235330276306131,-11.145370325612575 +CHEMBL3265031,CC1(O)CCN(c2ccc(Nc3nc(-c4ccc5cn[nH]c5c4)cn4ccnc34)cc2)CC1,-10.140252824399498,0.08108991524239104,-12.153887951643345 +CHEMBL3265037,COc1cc(Nc2nc(-c3ccc4cn[nH]c4c3)cn3ccnc23)ccc1N1CCOCC1,-10.926312452314724,0.06913724808597187,-12.843920517767115 +CHEMBL3265032,c1cn2cc(-c3ccc4cn[nH]c4c3)nc(Nc3ccc(N4CCOCC4)cc3)c2n1,-9.830932325125211,0.08279569027973459,-11.137577211218078 +CHEMBL3265033,O=S1(=O)CCN(c2ccc(Nc3nc(-c4ccc5cn[nH]c5c4)cn4ccnc34)cc2)CC1,-10.614207573293633,0.08846668409605196,-11.912163942029151 +CHEMBL3265034,c1cn2cc(-c3ccc4cn[nH]c4c3)nc(Nc3ccc(C4CCOCC4)cc3)c2n1,-9.259798121188416,0.07812055494781149,-11.558600249438788 +CHEMBL3265036,c1cn2cc(-c3ccc4cn[nH]c4c3)nc(Nc3ccc(N4CCCOCC4)cc3)c2n1,-9.97921660246026,0.09438825139675125,-10.482623277777673 diff --git a/summaries/dec_08_2025/merck/tnks2_neutral/README.md b/summaries/dec_08_2025/merck/tnks2_neutral/README.md new file mode 100644 index 0000000..348b399 --- /dev/null +++ b/summaries/dec_08_2025/merck/tnks2_neutral/README.md @@ -0,0 +1,38 @@ +# Tnks2 Neutral Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.61 +- RMSE: 0.80 +- R²: 0.56 +- Kendall 𝜏: 0.44 +- Spearman ρ: 0.60 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.17 Hours +- Total Nanoseconds Simulated: 3692.60 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/tnks2_neutral/ddg_results.csv b/summaries/dec_08_2025/merck/tnks2_neutral/ddg_results.csv new file mode 100644 index 0000000..19cc271 --- /dev/null +++ b/summaries/dec_08_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) +3a,3b,-1.5653567327062725,0.03793215368174313,-1.8251125869091867,0.03840441377010853,0.2597558542029141,0.05397913745106604,-0.5260493354729219 +1b,1a,0.47878864566688634,0.0464325219987892,-1.836924909639524,0.04802805364573124,2.3157135553064103,0.06680324121002873,1.3952195472505289 +1b,5a,-0.995190138205874,0.049951455742919655,0.2148720325407605,0.04861031456536701,-1.2100621707466346,0.06970014786914583,-0.8264598476524214 +1b,5b,-0.56689496772903,0.055385599657841,1.3497889194773642,0.05724844824095601,-1.9166838872063943,0.07965519113941072,-0.5405552764679439 +1a,5d,-4.633588772764377,0.06006035716291555,-1.545290701004639,0.06006606326318831,-3.088298071759739,0.08494220657879285,-2.349004747544686 +3a,5b,-8.261317378085227,0.050652771633263746,-8.59943486857719,0.050811009923034535,0.33811749049196127,0.07174581523357501,0.525340037635711 +1a,5c,0.010203148577185399,0.0673307029476363,3.533385942184575,0.06804498007200767,-3.5231827936073894,0.09572639590218969,-1.418601554367181 +3b,5d,-9.234474678227741,0.04012995511059259,-9.62877638710758,0.04036125707103466,0.39430170887984045,0.056916116957609834,0.6381594492824195 +3a,5c,-5.6929235261257265,0.06083600669737619,-6.448519713072256,0.06119204720542274,0.7555961869465291,0.08628723168623437,1.0425133069870027 +5a,5j,1.676259094181936,0.04625057384177254,2.177046072187078,0.048537421876777516,-0.5007869780051419,0.0670447380719586,-0.32791824345649395 +3b,5c,-4.0054161628634155,0.06143153631883908,-4.669624366550188,0.06260741470555112,0.6642082036867727,0.08771272445093531,1.5685626424599246 +5a,5k,-0.12398343648248115,0.046978919256111,0.281467907722687,0.04803545164562268,-0.40545134420516815,0.06718945951018769,-0.20612150628037756 +5a,7,-1.6752220903476247,0.0442306805664244,-4.035944220786664,0.04510356586947758,2.3607221304390396,0.06317186681990153,2.3763908249569816 +5b,5j,0.9409515352060992,0.03829715863177135,0.7812560696851995,0.039028513864061365,0.15969546552089978,0.05467995294167954,-0.6138228146409717 +5a,5n,4.177385476977155,0.06592621367671607,4.2729885464431066,0.06437805326441498,-0.09560306946595187,0.09214553375972097,0.04418056157028358 +5b,5h,7.676731289255743,0.055893437852927275,6.47134880296653,0.05522290960603695,1.2053824862892137,0.07857255335278071,0.42725797721099323 +5a,5p,9.954321409114586,0.07000411562051256,9.860547057027151,0.06683325517514198,0.09377435208743488,0.09678460725299108,0.25681759458173514 +5b,5k,-0.4610541017685562,0.05012775374793613,-0.8339819442787625,0.051302692259396425,0.3729278425102062,0.07172696793310072,-0.4920260774648552 +5b,5m,-1.2313476287236365,0.05616463992539117,-1.2031315993077503,0.05696702962974353,-0.028216029415886197,0.07999818274676569,-2.2282669178616215 +5b,7,-2.226364490646275,0.04961124439416902,-5.367341230779083,0.05248390388902067,3.1409767401328073,0.07222074312668021,2.090486253772504 +5d,5m,0.9298296819180711,0.049427602411574956,1.944192051412438,0.05039665360613682,-1.0143623694943669,0.07058973420302468,-1.815036994035408 +5d,5n,5.901391522101976,0.06173687110768693,5.98032171745837,0.06149189129096493,-0.07893019535639359,0.08713606571739968,0.17150591421201922 +5b,5p,8.927386945853806,0.06959247899208602,8.414140814178168,0.06903505483594312,0.5132461316756387,0.09802526168526972,-0.02908697660274251 +5e,5k,1.8458939503474026,0.04834341885100893,3.166827016287449,0.049656793746091256,-1.3209330659400464,0.06930283768610009,-0.8610754397207815 +5e,5h,9.944079934173082,0.0631032363960638,10.403860533217015,0.06434896470607204,-0.4597805990439329,0.09012662038710215,0.0582086149550669 +5e,7,0.14739844441308597,0.04736443609650538,-1.62952041676595,0.04843946915778239,1.776918861179036,0.0677478558998563,1.7214368915165779 +5f,5g,-3.399543754090451,0.0413880760296203,-2.6522913854393892,0.04193308843636119,-0.7472523686510618,0.058918220808552246,-0.5462602459540343 +5e,5i,3.058965636415549,0.061573483056396594,4.781851797797553,0.06165237027763269,-1.7228861613820041,0.087133854365262,-1.983493465476578 +5f,5i,-1.4006441021742355,0.032348703465694684,-1.2291921218547326,0.033780413651806306,-0.1714519803195027,0.046771304903739735,-1.827081136232103 +5f,5h,5.362633819318899,0.040071216442028525,4.3146107441326595,0.037909722662214394,1.0480230751862392,0.0551620291456896,0.21462094419954164 +5f,5l,0.8215566989863559,0.04096106774909229,1.57154877117953,0.04362126411781915,-0.7499920721931741,0.05983831343196652,0.17150591421201583 +5g,5a,0.6826901019406281,0.05429798123562529,-0.9014178212387413,0.055524954102383596,1.5841079231793693,0.07766138869693305,0.04771864175810509 +5l,5a,-3.4928476530625945,0.04666036680647072,-4.841228320626291,0.048284104852343704,1.3483806675636967,0.06714569689791385,-0.670047518407945 +5l,5b,-2.8856258754173614,0.04047064178323202,-3.5289561323542284,0.044142033136312216,0.6433302569368671,0.05988649209758384,-0.38414294722346737 +5i,5o,5.009987961895593,0.05745020252638494,4.637459740917841,0.05707783855512547,0.372528220977752,0.08098398251782642,0.04113111879943573 +5g,5b,1.4303729364107212,0.05787515281015327,0.5041587553087363,0.058767902538126394,0.9262141811019848,0.08248151114964683,0.33362321294258274 +5j,5o,3.106036830802186,0.07048152187020064,3.7854587406508746,0.07057183079856033,-0.6794219098486886,0.09973980262362762,-0.9594901697802442 +5o,5m,-6.0286583498823845,0.05155987945785053,-6.754175443073127,0.05065819706367977,0.7255170931907424,0.07228190713761426,-0.6549539334404056 +5p,5n,-4.693066421251007,0.05575380856554598,-5.000835540176047,0.05362102217861292,0.30776911892504,0.0773543870057985,-0.21263703301145156 diff --git a/summaries/dec_08_2025/merck/tnks2_neutral/dg_plot.png b/summaries/dec_08_2025/merck/tnks2_neutral/dg_plot.png new file mode 100644 index 0000000..fadf8c2 Binary files /dev/null and b/summaries/dec_08_2025/merck/tnks2_neutral/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/tnks2_neutral/dg_results.csv b/summaries/dec_08_2025/merck/tnks2_neutral/dg_results.csv new file mode 100644 index 0000000..bb490a2 --- /dev/null +++ b/summaries/dec_08_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) +3a,CC(C)(C)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-11.41195651590234,0.045310173288298915,-11.064783886058404 +3b,CC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-11.045263602214042,0.046102102999004704,-11.590833221531327 +1b,COc1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-9.445444760996281,0.04314662698960108,-9.99888857195475 +1a,O=c1[nH]c(-c2ccccc2)nc2ccccc12,-7.179885115142849,0.05476584504492018,-8.603669024704221 +5a,CC(C)(O)c1ccc(-c2nc3ccccc3c(=O)[nH]2)cc1,-10.63349474941307,0.02808138813872255,-10.825348419607172 +5b,CC(C)(O)c1ccc(-c2nc3cccc(F)c3c(=O)[nH]2)cc1,-11.319569783811405,0.024797048672794173,-10.539443848422694 +5d,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.450753427173252,0.040964726043371015,-10.952673772248907 +5c,CC(C)(O)c1ccc(-c2nc3cccc(Cl)c3c(=O)[nH]2)cc1,-10.57418176831573,0.047151465958973016,-10.022270579071401 +5j,CC(C)(O)c1ccc(-c2nc3ccc(F)c(F)c3c(=O)[nH]2)cc1,-11.133200584294949,0.0388697803390109,-11.153266663063665 +5k,CC(C)(O)c1ccc(-c2nc3c(F)cc(F)cc3c(=O)[nH]2)cc1,-11.062046325131897,0.043985167295254084,-11.03146992588755 +7,CC(C)(O)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)nc1,-8.187249953970964,0.04121458098021956,-8.448957594650189 +5n,CC(C)(OCCO)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.553024368466023,0.0497173161445308,-10.781167858036888 +5h,COc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-10.293431680793908,0.04424246801142716,-10.1121858712117 +5p,COCCOC(C)(C)c1ccc(-c2nc3ccc(F)cc3c(=O)[nH]2)cc1,-10.755104188545168,0.0539544599004727,-10.568530825025436 +5m,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.267923057849405,0.04397193475813541,-12.767710766284315 +5e,CC(C)(O)c1ccc(-c2nc3ccc(Cl)cc3c(=O)[nH]2)cc1,-9.873425178736754,0.04302400909898775,-10.170394486166767 +5f,CC(C)(O)c1ccc(-c2nc3c(F)cccc3c(=O)[nH]2)cc1,-11.414900626857339,0.0379357149947013,-10.326806815411242 +5g,CC(C)(O)c1ccc(-c2nc3c(Cl)cccc3c(=O)[nH]2)cc1,-12.197912457178543,0.04183563475069037,-10.873067061365276 +5i,Cc1cccc2c(=O)[nH]c(-c3ccc(C(C)(C)O)cc3)nc12,-11.692537717198615,0.04516006556769776,-12.153887951643345 +5l,CC(C)(O)c1ccc(-c2nc3c(F)ccc(F)c3c(=O)[nH]2)cc1,-12.040628452249626,0.037922198649071946,-10.155300901199226 +5o,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C(C)(C)OCCO)cc3)nc12,-11.721480562146196,0.05225292677858248,-12.112756832843909 diff --git a/summaries/dec_08_2025/merck/tnks2_positive/README.md b/summaries/dec_08_2025/merck/tnks2_positive/README.md new file mode 100644 index 0000000..3d729fc --- /dev/null +++ b/summaries/dec_08_2025/merck/tnks2_positive/README.md @@ -0,0 +1,38 @@ +# Tnks2 Positive Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.09 +- RMSE: 1.23 +- R²: 0.03 +- Kendall 𝜏: 0.33 +- Spearman ρ: 0.37 + +## 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 4090 +- MPS Processes: 12 +- Total Wallclock Time: 2.70 Hours +- Total Nanoseconds Simulated: 1169.80 +- TMD Forcefield: smirnoff_2_2_1_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_08_2025/merck/tnks2_positive/ddg_results.csv b/summaries/dec_08_2025/merck/tnks2_positive/ddg_results.csv new file mode 100644 index 0000000..15bb3f0 --- /dev/null +++ b/summaries/dec_08_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,-0.5378210533962827,0.04762782976076677,-1.6780319030751827,0.050046717964519025,1.1402108496788999,0.06908751078697721,1.1309960839922617 +8e,8b,9.708617504916623,0.05194094716894147,8.425682763540735,0.05211132699424923,1.2829347413758871,0.07357616729558789,-1.6968044668607012 +8d,8f,9.844523617705624,0.05615978929675709,9.591902723566388,0.05637176786170145,0.25262089413923594,0.0795719683413054,0.6826875274826852 +8b,8d,-19.848869741722876,0.06405946432361401,-17.87883826644885,0.06234169769990169,-1.9700314752740278,0.08938737182362116,-0.563054730112017 +8e,8f,-0.1778589451855968,0.032480883535931315,0.19610319754760883,0.03270262643012511,-0.3739621427332056,0.04609196861388165,-1.5771716694900328 +8d,8c,-0.25605715404274304,0.08042007588578824,-0.0991175921222558,0.08050735198884983,-0.15693956192048727,0.11379289226367567,2.381237719637223 +8c,8a,17.22081549346167,0.08534823802594114,15.474885592900655,0.08276774596310664,1.7459299005610158,0.1188899554459756,-0.6871869055329446 +8f,8a,9.41052008238467,0.05740462054998596,6.581461621975794,0.06002949891389977,2.8290584604088753,0.08305920298402678,1.0113632866215934 +8e,8c,-9.604621985431004,0.08191750561672971,-10.04870610741016,0.08136417266797803,0.44408412197915537,0.11545824492175294,0.12137852266450505 diff --git a/summaries/dec_08_2025/merck/tnks2_positive/dg_plot.png b/summaries/dec_08_2025/merck/tnks2_positive/dg_plot.png new file mode 100644 index 0000000..d38bd7a Binary files /dev/null and b/summaries/dec_08_2025/merck/tnks2_positive/dg_plot.png differ diff --git a/summaries/dec_08_2025/merck/tnks2_positive/dg_results.csv b/summaries/dec_08_2025/merck/tnks2_positive/dg_results.csv new file mode 100644 index 0000000..18cbf81 --- /dev/null +++ b/summaries/dec_08_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,-10.489684776465378,0.03654441636193259,-12.004063145357538 +8a,C[NH+]1CCN(c2ccc(-c3nc4ccc(F)cc4c(=O)[nH]3)cc2)CC1,-9.440345890545798,0.04348507205301499,-10.873067061365276 +8e,C[N@H+]1CC[C@H](c2ccc(-c3nc4c(F)cc(F)cc4c(=O)[nH]3)cc2)CC1,-11.81962720504244,0.034453952560536814,-10.307258678496837 +8d,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc(C4CC[NH2+]CC4)cc3)nc12,-12.238215342659863,0.04567470691144437,-12.567117875469554 +8f,Cc1cc(F)cc2c(=O)[nH]c(-c3ccc([C@H]4CC[N@H+](C)CC4)cc3)nc12,-12.165331299065246,0.03356882377933813,-11.88443034798687 +8c,O=c1[nH]c(-c2ccc(C3CC[NH2+]CC3)cc2)nc2c(F)cc(F)cc12,-11.668612750729675,0.048973633967836785,-10.185880155832331