Add December 8th Summary

summaries/dec_08_2025/README.md

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+# 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

summaries/dec_08_2025/jacs/cdk2/README.md

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+# 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

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

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

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