diff --git a/summaries/2026_mar_25/README.md b/summaries/2026_mar_25/README.md new file mode 100644 index 0000000..39b52e1 --- /dev/null +++ b/summaries/2026_mar_25/README.md @@ -0,0 +1,13 @@ +# Summary +- Number of Datasets: 14 +- Number of Ligands: 353 +- Number of Edges: 607 +- Total Wallclock Time: 351.11 Hours +- Average Time Per Edge: 0.58 Hours +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) + +![Retrospective dG performance](dg_plot.png) + +## Notes: +- A subset of the datasets run with dynamically sized water boxes (https://github.com/tmd-industries/tmd/pull/94) +- Wallclock time for some datasets is off due to running out of disk space during the intitial run diff --git a/summaries/2026_mar_25/dg_plot.png b/summaries/2026_mar_25/dg_plot.png new file mode 100644 index 0000000..93077ff Binary files /dev/null and b/summaries/2026_mar_25/dg_plot.png differ diff --git a/summaries/2026_mar_25/fragments/mcl1/README.md b/summaries/2026_mar_25/fragments/mcl1/README.md new file mode 100644 index 0000000..2e6d02a --- /dev/null +++ b/summaries/2026_mar_25/fragments/mcl1/README.md @@ -0,0 +1,39 @@ +# Mcl1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.55 +- RMSE: 0.72 +- R²: 0.26 +- Kendall 𝜏: 0.27 +- Spearman ρ: 0.38 + +## System Details +- Ligands: 12 +- Host Atoms: 2428 +- Map Details: + - Edges: 20 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 19 + - Mean Dummy Atoms: 7.2 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.62 Hours +- Average Time Per Edge: 0.18 Hours +- Total Nanoseconds Simulated: 2007.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/fragments/mcl1/ddg_results.csv b/summaries/2026_mar_25/fragments/mcl1/ddg_results.csv new file mode 100644 index 0000000..a8192fe --- /dev/null +++ b/summaries/2026_mar_25/fragments/mcl1/ddg_results.csv @@ -0,0 +1,21 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,15,5.414377300351039,0.06457087607262701,4.92091090597578,0.0595328048242698,-0.2699999999999996,0.49346639437525996,0.08782683466362179,0.3735861800011282,0.07390970286288413 +11,14,-0.32393759803494127,0.06288918326083696,-1.324761245045128,0.06242950099429511,-0.0600000000000005,1.0008236470101868,0.0886142875929826,1.001357518526012,0.0730428425216689 +2,13 flipped,9.805732856989476,0.054769429939795035,7.621378216978718,0.05438437274791764,0.1200000000000001,2.184354640010759,0.07718387432044703,1.7684387338892846,0.05478833777010601 +2,14,7.3815780392442285,0.06608764128091692,7.200699304390168,0.06446121604375969,-0.28000000000000025,0.18087873485406022,0.09231914592280095,-0.016147151056110864,0.05403385777115431 +2,15,19.613284678014328,0.07223852553659298,20.50615185340026,0.06899544333964779,0.020000000000000462,-0.8928671753859327,0.09989382249836844,-0.24129258901693174,0.0598540791976062 +2,3,0.49952108975603976,0.04307962616632179,2.2674712478375794,0.04501217819894488,-1.0599999999999996,-1.7679501580815398,0.06230529974924771,-1.765625643061684,0.05826086956679544 +2,4,-4.37090664544144,0.04177609693964057,-3.757010616181308,0.041144244576848954,-0.47999999999999954,-0.6138960292601318,0.05863523801699633,-0.615721012828609,0.052101439785242454 +2,5,-0.019201811794486236,0.043628111657551906,0.11172939014493247,0.042998621401803584,-0.71,-0.1309312019394187,0.06125596762160777,-0.027484250042722813,0.052642991925706636 +3,11,7.061484126893448,0.06217221406725052,6.287833170504798,0.062276228225281643,0.8399999999999999,0.7736509563886494,0.08799836818936695,0.7481209734795611,0.0762228835763325 +3,4,-4.825160975104707,0.05331762713971417,-5.953344337159753,0.05227793059282051,0.5800000000000001,1.1281833620550463,0.07467095413129085,1.1499046302330749,0.06613194487722354 +4,11,11.888021595957087,0.060772895251744063,12.315351929632866,0.06244089912200412,0.2599999999999998,-0.427330333675779,0.08713329260646444,-0.4017836567535138,0.07162512887044067 +5,10,15.08389166215939,0.06014287882741134,15.595605345656667,0.0627537583508613,1.0,-0.5117136834972758,0.08692065382178725,-0.5873945189753371,0.06820130482312287 +5,8,11.987033373391197,0.05662648514473795,13.1200772108599,0.0556392701067972,-0.33000000000000007,-1.1330438374687042,0.07938694601673732,-0.896165788533744,0.06078155659513949 +7,13 flipped,-4.599529250990518,0.04927927086874049,-5.888689748339937,0.04640034044784516,0.6699999999999999,1.2891604973494197,0.06768632159477002,1.3666028580020844,0.05728718438418723 +7,14,-6.660551378692329,0.053833501880447755,-6.109615722513587,0.05357332488864938,0.2699999999999996,-0.5509356561787419,0.07594831837728173,-0.41798302694331113,0.0565660439193866 +7,8,-1.3617545102866675,0.050159285792232555,-0.2467185559614011,0.04863832730667633,-0.4900000000000002,-1.1150359543252664,0.06986874003714565,-1.325485914463667,0.05420910790102557 +7,9,0.2353244277111983,0.053960713541693864,0.8500609769167551,0.053147374272155004,0.39999999999999947,-0.6147365492055568,0.07573903879739476,-0.5966236319216067,0.061583563539376114 +8,10,3.1066804788163846,0.05083630810495768,2.7706628132414557,0.04845238413245525,1.33,0.3360176655749291,0.07022794137564611,0.30877126955840684,0.06736988363545615 +9,13 flipped,-4.945964936863256,0.048560721718424585,-6.656673208935519,0.04913519870363419,0.27000000000000046,1.7107082720722626,0.06908264214301511,1.963226489923691,0.06912874147294089 +9,15,6.713363667695627,0.059270174271688084,6.428617724078294,0.056078033885336824,0.17000000000000082,0.2847459436173325,0.08159472680658512,-0.04650483298252528,0.07320882281948528 diff --git a/summaries/2026_mar_25/fragments/mcl1/dg_comparison_plot.png b/summaries/2026_mar_25/fragments/mcl1/dg_comparison_plot.png new file mode 100644 index 0000000..19760b9 Binary files /dev/null and b/summaries/2026_mar_25/fragments/mcl1/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/fragments/mcl1/dg_plot.png b/summaries/2026_mar_25/fragments/mcl1/dg_plot.png new file mode 100644 index 0000000..a712bb9 Binary files /dev/null and b/summaries/2026_mar_25/fragments/mcl1/dg_plot.png differ diff --git a/summaries/2026_mar_25/fragments/mcl1/dg_results.csv b/summaries/2026_mar_25/fragments/mcl1/dg_results.csv new file mode 100644 index 0000000..8df0ea4 --- /dev/null +++ b/summaries/2026_mar_25/fragments/mcl1/dg_results.csv @@ -0,0 +1,13 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +10,Cc1ccc2c(C)c(C(=O)[O-])oc2c1C,-6.012643996564674,0.05242004186617595,-5.04 +15,Cc1cccc2c(-c3ccccc3)c(C(=O)[O-])[nH]c12,-5.639057816563546,0.05210358325516762,-5.31 +11,O=C([O-])c1cc2c(Br)cc(Cl)cc2o1,-6.415269897128737,0.05730031820659568,-5.55 +14,Cn1c(C(=O)[O-])cc2cc(Br)ccc21,-5.413912378602725,0.04529823812322287,-5.61 +2,O=C([O-])c1sc2ccccc2c1Cl,-5.397765227546614,0.029457213183957706,-5.33 +13 flipped,Cn1c(C(=O)[O-])cc2ccccc21,-3.6293264936573295,0.04619561177261422,-5.21 +3,O=C([O-])c1sc2cccc(Cl)c2c1Cl,-7.163390870608298,0.05026531124059632,-6.39 +4,O=C([O-])c1sc2cc(Cl)ccc2c1Cl,-6.013486240375223,0.042974790507111414,-5.81 +5,Cc1ccc2c(Cl)c(C(=O)[O-])sc2c1,-5.425249477589337,0.043629774126448126,-6.04 +8,Cc1c(C(=O)[O-])oc2cc(Cl)ccc12,-6.321415266123081,0.042318322648744744,-6.37 +7,Cc1c(C(=O)[O-])oc2ccc(Cl)cc12,-4.995929351659414,0.033879004525247954,-5.88 +9,Cc1c(C(=O)[O-])oc2c(C)cccc12,-5.592552983581021,0.05142711687997495,-5.48 diff --git a/summaries/2026_mar_25/fragments/p38/README.md b/summaries/2026_mar_25/fragments/p38/README.md new file mode 100644 index 0000000..faf07a3 --- /dev/null +++ b/summaries/2026_mar_25/fragments/p38/README.md @@ -0,0 +1,39 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.76 +- RMSE: 0.87 +- R²: 0.89 +- Kendall 𝜏: 0.73 +- Spearman ρ: 0.89 + +## System Details +- Ligands: 6 +- Host Atoms: 7065 +- Map Details: + - Edges: 10 + - Min Dummy Atoms: 4 + - Max Dummy Atoms: 32 + - Mean Dummy Atoms: 19.6 + - Median Dummy Atoms: 20.5 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 3.68 Hours +- Average Time Per Edge: 0.37 Hours +- Total Nanoseconds Simulated: 1327.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/fragments/p38/ddg_results.csv b/summaries/2026_mar_25/fragments/p38/ddg_results.csv new file mode 100644 index 0000000..ec47cc7 --- /dev/null +++ b/summaries/2026_mar_25/fragments/p38/ddg_results.csv @@ -0,0 +1,11 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +1_1W7H,3,24.430898761678122,0.04788938647581076,23.76076092448228,0.04887164003735272,-0.1499999999999999,0.6701378371958422,0.06842390325734234,0.6698770401310097,0.04774679250108025 +1_1W7H,5_1WBW,7.2286107581426196,0.0635611147734271,9.553458900345417,0.06147948374421008,-2.0000000000000004,-2.324848142202797,0.08842930641306289,-2.4672171284341453,0.05628380518080255 +1_1W7H,6,3.0290489275099204,0.06864172836091006,5.39164764945018,0.07126660798281463,-1.1,-2.3625987219402593,0.09894754310112579,-2.18380193014417,0.05775252723087723 +4,3,27.816111505983635,0.05843091334780482,24.627815710607177,0.057923315699726176,1.3100000000000005,3.18829579537646,0.0822756472858696,3.589054222024915,0.05039019046097695 +4,5_1WBW,10.512071006802866,0.06416426878289874,10.283943686233378,0.061487730520289566,-0.54,0.22812732056948767,0.08886953579815651,0.45196005345975987,0.05854299126439352 +4,7,9.558682032897066,0.07184021927010815,9.809233392132136,0.07004325382212585,-0.8999999999999995,-0.2505513592350693,0.10033481205826802,-1.1318600091010582,0.06454740357452685 +5_1WBW,3,17.091420698806427,0.0685147115459836,14.046813133546074,0.06656850249210051,1.8500000000000005,3.0446075652603524,0.09552816978394452,3.137094168565155,0.054095801780668744 +6,3,20.9553543722249,0.06529752891043908,18.407732057334012,0.065342732401627,0.9500000000000002,2.5476223148908868,0.09237662019970348,2.8536789702751797,0.05562232866588817 +6,7,2.639382360861954,0.07620949660699415,4.308814210568148,0.07367972820131477,-1.2599999999999998,-1.6694318497061933,0.10600278166591229,-1.8672352608507934,0.06870982069351798 +7,3,20.281579229291463,0.06899997841436346,14.56095953919259,0.06889615633299423,2.21,5.720619690098874,0.09750731961572427,4.720914231125973,0.06054288771047669 diff --git a/summaries/2026_mar_25/fragments/p38/dg_comparison_plot.png b/summaries/2026_mar_25/fragments/p38/dg_comparison_plot.png new file mode 100644 index 0000000..2c6b54b Binary files /dev/null and b/summaries/2026_mar_25/fragments/p38/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/fragments/p38/dg_plot.png b/summaries/2026_mar_25/fragments/p38/dg_plot.png new file mode 100644 index 0000000..a4d3dd0 Binary files /dev/null and b/summaries/2026_mar_25/fragments/p38/dg_plot.png differ diff --git a/summaries/2026_mar_25/fragments/p38/dg_results.csv b/summaries/2026_mar_25/fragments/p38/dg_results.csv new file mode 100644 index 0000000..848154c --- /dev/null +++ b/summaries/2026_mar_25/fragments/p38/dg_results.csv @@ -0,0 +1,7 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +1_1W7H,Nc1ncccc1OCc1ccccc1,-3.293107268110638,0.03550540205009898,-3.94 +3,c1ccc(COc2cccnc2)cc1,-2.6232302279796285,0.03192369996416519,-4.09 +5_1WBW,Nc1ncccc1OCc1cccc2ccccc12,-5.7603243965447835,0.04367188055134978,-5.94 +6,OCCNc1ccc(OCc2c(Cl)cccc2Cl)cn1,-5.476909198254808,0.04554910346882849,-5.04 +4,Nc1ncccc1OCc1c(Cl)cccc1Cl,-6.212284450004543,0.03898780162168024,-5.4 +7,CC(C)(CO)Nc1ccc(OCc2c(Cl)cccc2Cl)cn1,-7.3441444591056015,0.05144238168010253,-6.3 diff --git a/summaries/2026_mar_25/jacs_set/jnk1/README.md b/summaries/2026_mar_25/jacs_set/jnk1/README.md new file mode 100644 index 0000000..9755aec --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/jnk1/README.md @@ -0,0 +1,39 @@ +# Jnk1 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.23 +- RMSE: 1.36 +- R²: 0.53 +- Kendall 𝜏: 0.58 +- Spearman ρ: 0.73 + +## System Details +- Ligands: 21 +- Host Atoms: 5993 +- Map Details: + - Edges: 36 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 13 + - Mean Dummy Atoms: 6.5 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 7.10 Hours +- Average Time Per Edge: 0.20 Hours +- Total Nanoseconds Simulated: 3245.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/jacs_set/jnk1/ddg_results.csv b/summaries/2026_mar_25/jacs_set/jnk1/ddg_results.csv new file mode 100644 index 0000000..ebe9b7c --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/jnk1/ddg_results.csv @@ -0,0 +1,37 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +17124-1,18631-1,-3.8647727515714645,0.054885792932781126,-5.835118787534282,0.05560481578007555,0.2699999999999996,1.9703460359628173,0.07813031296363958,2.093299213377218,0.061833957222889126 +17124-1,18637-1,-8.737563809900557,0.05878238191556125,-8.64116002762175,0.059117852092238625,-0.46000000000000085,-0.09640378227880807,0.08336839244981702,-0.3621144989218372,0.07502603953294852 +17124-1,18652-1,-15.852860768562692,0.05806034019583097,-14.544529721057774,0.05733720936193133,-1.0,-1.3083310475049175,0.08159999191831806,-1.228035812513827,0.07424175296587847 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index 0000000..867ed23 Binary files /dev/null and b/summaries/2026_mar_25/jacs_set/jnk1/dg_plot.png differ diff --git a/summaries/2026_mar_25/jacs_set/jnk1/dg_results.csv b/summaries/2026_mar_25/jacs_set/jnk1/dg_results.csv new file mode 100644 index 0000000..e91a19c --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/jnk1/dg_results.csv @@ -0,0 +1,22 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +17124-1,CCOc1nc(NC(=O)Cc2cc(OC)c(Br)cc2OC)cc(N)c1C#N,-10.812984785483142,0.05019543524270668,-9.68 +18631-1,CCOc1nc(NC(=O)Cc2ccccc2OC)cc(N)c1C#N,-8.719685572105924,0.03610895382917266,-9.41 +18637-1,CCOc1nc(NC(=O)Cc2cc(OC)c(NC(C)=O)cc2OC)cc(N)c1C#N,-11.175099284404979,0.05576132072319302,-10.14 +18652-1,COc1cc(S(C)(=O)=O)c(OC)cc1CC(=O)Nc1cc(N)c(C#N)c(OC(C)C)n1,-12.041020597996969,0.05470151884766789,-10.68 +18660-1,COc1ccc(OC)c(CC(=O)Nc2cc(N)c(C#N)c(OCCS(C)(=O)=O)n2)c1,-11.756963215732654,0.057185123042364595,-8.7 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+ +## System Details +- Ligands: 42 +- Host Atoms: 2542 +- Map Details: + - Edges: 73 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.7 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 13.77 Hours +- Average Time Per Edge: 0.19 Hours +- Total Nanoseconds Simulated: 7257.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/jacs_set/mcl1/ddg_results.csv b/summaries/2026_mar_25/jacs_set/mcl1/ddg_results.csv new file mode 100644 index 0000000..7188816 --- 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b/summaries/2026_mar_25/jacs_set/mcl1/dg_comparison_plot.png new file mode 100644 index 0000000..995b6fb Binary files /dev/null and b/summaries/2026_mar_25/jacs_set/mcl1/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/jacs_set/mcl1/dg_plot.png b/summaries/2026_mar_25/jacs_set/mcl1/dg_plot.png new file mode 100644 index 0000000..b56c5aa Binary files /dev/null and b/summaries/2026_mar_25/jacs_set/mcl1/dg_plot.png differ diff --git a/summaries/2026_mar_25/jacs_set/mcl1/dg_results.csv b/summaries/2026_mar_25/jacs_set/mcl1/dg_results.csv new file mode 100644 index 0000000..4e06318 --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/mcl1/dg_results.csv @@ -0,0 +1,43 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +23,O=C([O-])c1sc2ccccc2c1CCCOc1cccc2ccccc12,-8.826967584494835,0.06110619672633892,-8.83 +44,O=C([O-])c1[nH]c2ccccc2c1CCCOc1ccc(Cl)c2ccccc12,-8.483297842881345,0.05335459566889519,-8.67 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a/summaries/2026_mar_25/jacs_set/p38/README.md b/summaries/2026_mar_25/jacs_set/p38/README.md new file mode 100644 index 0000000..0e45985 --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/p38/README.md @@ -0,0 +1,39 @@ +# P38 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.88 +- RMSE: 1.09 +- R²: 0.39 +- Kendall 𝜏: 0.43 +- Spearman ρ: 0.61 + +## System Details +- Ligands: 34 +- Host Atoms: 6680 +- Map Details: + - Edges: 60 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 22 + - Mean Dummy Atoms: 9.6 + - Median Dummy Atoms: 9.5 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 16.67 Hours +- Average Time Per Edge: 0.28 Hours +- Total Nanoseconds Simulated: 7186.00 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/jacs_set/p38/ddg_results.csv b/summaries/2026_mar_25/jacs_set/p38/ddg_results.csv new file mode 100644 index 0000000..d3d8dbc --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/p38/ddg_results.csv @@ -0,0 +1,61 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +2aa,2y,12.601361847223929,0.06611178452995209,12.756249367593096,0.06749991204702784,-0.5099999999999998,-0.15488752036916723,0.09448283537284063,-0.23286098147817036,0.10378055252514576 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differ diff --git a/summaries/2026_mar_25/jacs_set/p38/dg_plot.png b/summaries/2026_mar_25/jacs_set/p38/dg_plot.png new file mode 100644 index 0000000..3055f0d Binary files /dev/null and b/summaries/2026_mar_25/jacs_set/p38/dg_plot.png differ diff --git a/summaries/2026_mar_25/jacs_set/p38/dg_results.csv b/summaries/2026_mar_25/jacs_set/p38/dg_results.csv new file mode 100644 index 0000000..c899320 --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/p38/dg_results.csv @@ -0,0 +1,35 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +2aa,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CO)CO)nc21,-9.332639557435021,0.07632616560740095,-9.27 +2y,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NCC(C)(C)O)nc21,-9.565500538913192,0.07031869969002656,-9.78 +2z,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(C)(C)CO)nc21,-10.805891594787587,0.07042408906608078,-10.36 +3flw,Cn1c(=O)c(Oc2ccc(F)cc2F)cc2cnc(NC(CCO)CCO)nc21,-12.118282118580577,0.06295085088662257,-10.68 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+3fmk,C[C@@H](Cn1ncnn1)Nc1ncc2cc(Oc3ccc(F)cc3F)c(=O)n(C)c2n1,-11.994659475552849,0.0637009163776241,-11.83 diff --git a/summaries/2026_mar_25/jacs_set/ptp1b/README.md b/summaries/2026_mar_25/jacs_set/ptp1b/README.md new file mode 100644 index 0000000..fd1078f --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/ptp1b/README.md @@ -0,0 +1,39 @@ +# Ptp1B Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.04 +- RMSE: 1.87 +- R²: 0.33 +- Kendall 𝜏: 0.57 +- Spearman ρ: 0.70 + +## System Details +- Ligands: 23 +- Host Atoms: 5488 +- Map Details: + - Edges: 40 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 30 + - Mean Dummy Atoms: 11.2 + - Median Dummy Atoms: 11.5 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 12.44 Hours +- Average Time Per Edge: 0.31 Hours +- Total Nanoseconds Simulated: 5118.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/jacs_set/ptp1b/ddg_results.csv b/summaries/2026_mar_25/jacs_set/ptp1b/ddg_results.csv new file mode 100644 index 0000000..29c1dfe --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/ptp1b/ddg_results.csv @@ -0,0 +1,41 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) 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b/summaries/2026_mar_25/jacs_set/ptp1b/dg_comparison_plot.png new file mode 100644 index 0000000..267574b Binary files /dev/null and b/summaries/2026_mar_25/jacs_set/ptp1b/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/jacs_set/ptp1b/dg_plot.png b/summaries/2026_mar_25/jacs_set/ptp1b/dg_plot.png new file mode 100644 index 0000000..4b99253 Binary files /dev/null and b/summaries/2026_mar_25/jacs_set/ptp1b/dg_plot.png differ diff --git a/summaries/2026_mar_25/jacs_set/ptp1b/dg_results.csv b/summaries/2026_mar_25/jacs_set/ptp1b/dg_results.csv new file mode 100644 index 0000000..1c37ee8 --- /dev/null +++ b/summaries/2026_mar_25/jacs_set/ptp1b/dg_results.csv @@ -0,0 +1,24 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +20667,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Br,-12.50471165743132,0.06406692807189257,-11.42 +23482,CS(=O)(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-10.45356341205224,0.0548956825391234,-10.01 +23485,Cc1c(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc(C(=O)[O-])c1OCC(=O)[O-],-10.36728503477533,0.0658497545056136,-11.01 +23486,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)c1Cl,-13.304250587428397,0.06360417801942488,-12.47 +20669,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCc3ccccc3)c2)c1Br,-7.80787571483039,0.07022671313048764,-8.61 +23466,Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-5.294815580503224,0.06697311316250011,-7.85 +23330,CC1(C)CC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC(C)(C)C1,-9.251617265563748,0.06836337088710653,-10.13 +20670,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCC3)c2)c1Br,-8.085440806966737,0.05303448644928408,-9.08 +23475,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCC3)c2)c1Br,-8.173272194967167,0.05468973063010049,-8.72 +23472,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NS(=O)(=O)c3ccc(F)cc3)c2)c1Br,-7.086454700622237,0.06926432637620465,-8.65 +23467,COc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-5.765934429859904,0.05972116188252744,-7.34 +23473,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(OCc3ccccc3)c2)c1Br,-8.809263332498315,0.06790847578270004,-8.39 +23468,CCC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.4662677551250685,0.048640822598246224,-7.75 +23469,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC(=O)c3ccccc3)c2)c1Br,-7.840110229178748,0.08281491853746621,-7.72 +23471,COC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.48353641526266,0.060954571653246095,-7.75 +23474,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NCC3CCCCC3)c2)c1Br,-8.127716713809777,0.08368858715075661,-9.11 +23470,CC(C)NC(=O)Nc1cccc(-c2sc(C(=O)[O-])c(OCC(=O)[O-])c2Br)c1,-7.862936213874979,0.059506239670871264,-7.72 +23476,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCCCCC3)c2)c1Br,-9.086515339933813,0.06531858910355175,-9.41 +23477,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCOCC3)c2)c1Br,-8.536208502596548,0.04105547443756248,-8.85 +23479,CC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-8.93202916622543,0.06275179327734876,-9.14 +23483,O=C([O-])COc1c(C(=O)[O-])sc(-c2cccc(NC3CCN(S(=O)(=O)c4ccccc4)CC3)c2)c1Br,-10.276847578440233,0.0635199237386096,-9.87 +23480,COC(=O)N1CCC(Nc2cccc(-c3sc(C(=O)[O-])c(OCC(=O)[O-])c3Br)c2)CC1,-9.368939448351071,0.06509331653543553,-8.72 +23484,O=C([O-])COc1cc(-c2cccc(NC3CCN(S(=O)(=O)Cc4ccccc4)CC3)c2)sc1C(=O)[O-],-15.584407919702645,0.0633433720425641,-7.75 diff --git a/summaries/2026_mar_25/merck/cdk8/README.md b/summaries/2026_mar_25/merck/cdk8/README.md new file mode 100644 index 0000000..e288785 --- /dev/null +++ b/summaries/2026_mar_25/merck/cdk8/README.md @@ -0,0 +1,39 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.60 +- RMSE: 1.88 +- R²: 0.70 +- Kendall 𝜏: 0.67 +- Spearman ρ: 0.85 + +## System Details +- Ligands: 32 +- Host Atoms: 11038 +- Map Details: + - Edges: 57 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 20 + - Mean Dummy Atoms: 10.7 + - Median Dummy Atoms: 10.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 120.65 Hours +- Average Time Per Edge: 2.12 Hours +- Total Nanoseconds Simulated: 7201.60 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/cdk8/ddg_results.csv b/summaries/2026_mar_25/merck/cdk8/ddg_results.csv new file mode 100644 index 0000000..c85b8d7 --- /dev/null +++ b/summaries/2026_mar_25/merck/cdk8/ddg_results.csv @@ -0,0 +1,58 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +13,42-flipped,18.504571201572748,0.07159825070300123,21.247633236088348,0.07046918138169188,-0.24160000000000004,-2.743062034515601,0.10046001706318591,-3.062288023983225,0.11782606552605403 +14,16-flipped,4.4004913138947535,0.0731845190946759,7.522032109436192,0.06964078374388909,-0.9521699999999989,-3.121540795541438,0.10102382192127808,-3.537533573385499,0.16020364411802182 +14,17-flipped,-2.8717835094583672,0.07637934434682377,-0.36890221154624697,0.07173219900383754,-0.6547699999999992,-2.50288129791212,0.10478221517403052,-2.8979362420406813,0.14606409176802784 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Atoms: 5906 +- Map Details: + - Edges: 15 + - Min Dummy Atoms: 2 + - Max Dummy Atoms: 27 + - Mean Dummy Atoms: 11.9 + - Median Dummy Atoms: 8.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.11 Hours +- Average Time Per Edge: 0.27 Hours +- Total Nanoseconds Simulated: 1670.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/eg5_neutral/ddg_results.csv b/summaries/2026_mar_25/merck/eg5_neutral/ddg_results.csv new file mode 100644 index 0000000..3d5dd47 --- /dev/null +++ b/summaries/2026_mar_25/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),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL1078691,CHEMBL1078998,5.774724134534203,0.0624819163077263,4.489970300130638,0.06266747664439926,-0.18320000000000114,1.284753834403565,0.08849408169172693,1.100480961879585,0.0635812650743407 +CHEMBL1078691,CHEMBL1084115,4.105612215928864,0.061356455120967955,1.8136592493462462,0.06022106338774547,0.7516800000000003,2.2919529665826186,0.0859720365035179,1.6506298820398477,0.06362559957712764 +CHEMBL1078774,CHEMBL1078691,0.06061794439842223,0.04280578525180274,-0.7801256290585403,0.04257674703932666,0.4131,0.8407435734569625,0.06037478479857518,0.44722050271087355,0.056456969572626345 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Binary files /dev/null and b/summaries/2026_mar_25/merck/eg5_neutral/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/merck/eg5_neutral/dg_plot.png b/summaries/2026_mar_25/merck/eg5_neutral/dg_plot.png new file mode 100644 index 0000000..7709db5 Binary files /dev/null and b/summaries/2026_mar_25/merck/eg5_neutral/dg_plot.png differ diff --git a/summaries/2026_mar_25/merck/eg5_neutral/dg_results.csv b/summaries/2026_mar_25/merck/eg5_neutral/dg_results.csv new file mode 100644 index 0000000..5ad4047 --- /dev/null +++ b/summaries/2026_mar_25/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,-11.351650303204307,0.040113349304561015,-10.2494 +CHEMBL1078998,CC(C)(C)c1ccc2c(c1)[C@H]1OCCC[C@H]1[C@H](c1cccs1)N2,-10.251169341324722,0.049330482219656545,-10.4326 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--- /dev/null +++ b/summaries/2026_mar_25/merck/eg5_positive_1/README.md @@ -0,0 +1,39 @@ +# Eg5 Map Charge 1 + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.93 +- RMSE: 1.12 +- R²: 0.02 +- Kendall 𝜏: 0.02 +- Spearman ρ: 0.13 + +## System Details +- Ligands: 19 +- Host Atoms: 5906 +- Map Details: + - Edges: 31 + - Min Dummy Atoms: 5 + - Max Dummy Atoms: 36 + - Mean Dummy Atoms: 16.8 + - Median Dummy Atoms: 16.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 11.19 Hours +- Average Time Per Edge: 0.36 Hours +- Total Nanoseconds Simulated: 4722.80 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/eg5_positive_1/ddg_results.csv b/summaries/2026_mar_25/merck/eg5_positive_1/ddg_results.csv new file mode 100644 index 0000000..b7003b7 --- /dev/null +++ b/summaries/2026_mar_25/merck/eg5_positive_1/ddg_results.csv @@ -0,0 +1,32 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +CHEMBL1077204,CHEMBL1084676,8.34070695794329,0.05844968983636203,8.608778883069071,0.0609281741219357,0.3335000000000008,-0.2680719251257804,0.08443108813582731,-0.18336784697448394,0.11410736559353489 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0000000..195f93f Binary files /dev/null and b/summaries/2026_mar_25/merck/eg5_positive_1/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/merck/eg5_positive_1/dg_plot.png b/summaries/2026_mar_25/merck/eg5_positive_1/dg_plot.png new file mode 100644 index 0000000..7b7d67c Binary files /dev/null and b/summaries/2026_mar_25/merck/eg5_positive_1/dg_plot.png differ diff --git a/summaries/2026_mar_25/merck/eg5_positive_1/dg_results.csv b/summaries/2026_mar_25/merck/eg5_positive_1/dg_results.csv new file mode 100644 index 0000000..44881f7 --- /dev/null +++ b/summaries/2026_mar_25/merck/eg5_positive_1/dg_results.csv @@ -0,0 +1,20 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +CHEMBL1077204,C[NH+](C)CCNC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.10109994250756,0.07902680538134475,-11.1117 +CHEMBL1084676,C[NH+](C)CCOC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-11.284467789482044,0.08231193664296625,-10.7782 +CHEMBL1085692,C[NH+](C)CCCC(=O)NC[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-10.402214311488544,0.0668981197452754,-11.3918 +CHEMBL1077227,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1cccs1,-10.622365395155484,0.06717764944772657,-11.3918 +CHEMBL1084935,CC[N@H+](CCO)C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-8.787155366806136,0.06893507192167997,-10.5962 +CHEMBL1086410,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(C)(C)C)ccc1N[C@H]2c1ccccc1,-10.360101795651113,0.07107683599506058,-11.5248 +CHEMBL1082248,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-10.180521858113822,0.051874534421064454,-11.6963 +CHEMBL1083517,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccc(O)cc1,-13.3009712446875,0.05991403643510624,-11.5248 +CHEMBL1096002,OCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Cl)cc(F)c1N[C@H]2c1ccccc1,-10.727786364049628,0.05064599211833567,-11.1913 +CHEMBL1082249,CC(=O)NCC[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(Br)cc(F)c1N[C@H]2c1ccccc1,-10.538740258852158,0.06355908697684944,-11.2832 +CHEMBL1083836,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C3CC3)ccc1N[C@H]2c1ccccc1,-11.202222519179,0.06590797863176881,-10.9219 +CHEMBL1085666,[NH3+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1,-9.797738135180898,0.07001080944795965,-10.5656 +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,-12.043544028244682,0.08589708913694848,-11.938 +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,-11.163595101788202,0.07043070475489438,-9.86313 +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,-12.333805674048364,0.08437842063478972,-11.5248 +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,-11.310398817443335,0.06792319965734352,-11.938 +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+],-12.520504109737116,0.06604441173808884,-11.1913 +CHEMBL1086409,C[NH2+]C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccc(F)cc1,-12.37103584295267,0.06632363644144992,-9.93104 +CHEMBL1093087,[NH3+]CCN(C[C@H]1CC[C@@H]2[C@H](O1)c1cc(C(F)(F)F)ccc1N[C@H]2c1ccccc1)c1ccccc1,-10.911801444631742,0.07749296728739614,-10.5962 diff --git a/summaries/2026_mar_25/merck/hif2a/README.md b/summaries/2026_mar_25/merck/hif2a/README.md new file mode 100644 index 0000000..1dc71c3 --- /dev/null +++ b/summaries/2026_mar_25/merck/hif2a/README.md @@ -0,0 +1,39 @@ +# Hif2A Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.68 +- RMSE: 1.97 +- R²: 0.12 +- Kendall 𝜏: 0.19 +- Spearman ρ: 0.26 + +## System Details +- Ligands: 41 +- Host Atoms: 1770 +- Map Details: + - Edges: 70 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 12 + - Mean Dummy Atoms: 4.6 + - Median Dummy Atoms: 4.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 12.57 Hours +- Average Time Per Edge: 0.18 Hours +- Total Nanoseconds Simulated: 7180.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/hif2a/ddg_results.csv b/summaries/2026_mar_25/merck/hif2a/ddg_results.csv new file mode 100644 index 0000000..2db0078 --- /dev/null +++ b/summaries/2026_mar_25/merck/hif2a/ddg_results.csv @@ -0,0 +1,71 @@ +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),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +124,227,12.988896953805792,0.0679830788375272,12.150002620525111,0.06721443900667196,-0.6355000000000004,0.838894333280681,0.09560062666746001,0.5425121676400835,0.08699481995979833 +155,156,1.934330365576921,0.04052948539584359,2.3921774432569145,0.04113816236450389,0.7671099999999988,-0.4578470776799934,0.05774935141783138,-0.38803331660914786,0.09467442469912539 +15,167,-8.80698142672754,0.053113170078045835,-11.094817443249253,0.051358549657944313,0.3725000000000005,2.2878360165217124,0.07388307965093872,1.846944785901126,0.06691707070642484 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b/summaries/2026_mar_25/merck/hif2a_jmc2023/README.md @@ -0,0 +1,39 @@ +# Hif2A Jmc2023 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.27 +- RMSE: 1.43 +- R²: 0.51 +- Kendall 𝜏: 0.56 +- Spearman ρ: 0.75 + +## System Details +- Ligands: 38 +- Host Atoms: 1937 +- Map Details: + - Edges: 62 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 15 + - Mean Dummy Atoms: 5.8 + - Median Dummy Atoms: 5.5 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 10.35 Hours +- Average Time Per Edge: 0.17 Hours +- Total Nanoseconds Simulated: 5877.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/hif2a_jmc2023/ddg_results.csv b/summaries/2026_mar_25/merck/hif2a_jmc2023/ddg_results.csv new file mode 100644 index 0000000..2bd89a2 --- /dev/null +++ b/summaries/2026_mar_25/merck/hif2a_jmc2023/ddg_results.csv @@ -0,0 +1,63 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +19a-bindingpose1,19b,-3.343223975196449,0.04352023524547419,-3.4009148109335876,0.039884803422162156,-0.07620975148280174,0.05769083573713828,0.05903226592166296,0.07460986349924958,0.0931115992176715 +19a-bindingpose1,19c-bindingpose2,-3.80023699507486,0.04719682333742887,-4.013559119961125,0.0446701142291551,-0.024336634641450416,0.2133221248862658,0.06498429993767907,0.4221452754130217,0.09386421292060787 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b/summaries/2026_mar_25/merck/pfkfb3/README.md @@ -0,0 +1,39 @@ +# Pfkfb3 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 0.86 +- RMSE: 1.09 +- R²: 0.39 +- Kendall 𝜏: 0.43 +- Spearman ρ: 0.59 + +## System Details +- Ligands: 40 +- Host Atoms: 8158 +- Map Details: + - Edges: 71 + - Min Dummy Atoms: 0 + - Max Dummy Atoms: 17 + - Mean Dummy Atoms: 4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 73.44 Hours +- Average Time Per Edge: 1.03 Hours +- Total Nanoseconds Simulated: 7007.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/pfkfb3/ddg_results.csv b/summaries/2026_mar_25/merck/pfkfb3/ddg_results.csv new file mode 100644 index 0000000..b036f99 --- /dev/null +++ b/summaries/2026_mar_25/merck/pfkfb3/ddg_results.csv @@ -0,0 +1,72 @@ +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),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +19,23,-3.924539778650978,0.03841343952963557,-2.898614521832554,0.03810536245686535,-0.3636700000000008,-1.0259252568184243,0.05410740230750365,-1.079774806967432,0.10357648023334425 +19,33,-5.621174129882846,0.04856785969800043,-2.720744798312322,0.05026401295027965,-1.0561300000000005,-2.9004293315705234,0.06989497831397143,-2.758748892576011,0.09713067279458007 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diff --git a/summaries/2026_mar_25/merck/pfkfb3/dg_plot.png b/summaries/2026_mar_25/merck/pfkfb3/dg_plot.png new file mode 100644 index 0000000..20e063f Binary files /dev/null and b/summaries/2026_mar_25/merck/pfkfb3/dg_plot.png differ diff --git a/summaries/2026_mar_25/merck/pfkfb3/dg_results.csv b/summaries/2026_mar_25/merck/pfkfb3/dg_results.csv new file mode 100644 index 0000000..0ad33f8 --- /dev/null +++ b/summaries/2026_mar_25/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,-6.530661846878229,0.07273772676947522,-7.55079 +23,Cn1ccc2ccc(-c3cc(Nc4cccnc4)cc4nccnc34)cc21,-7.610436653845661,0.07373812014106082,-7.914460000000001 +33,Cn1ccc2ccc(-c3cc(Nc4cnccc4C#N)cc4nccnc34)cc21,-9.28941073945424,0.06437072861120142,-8.60692 +20,COc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-8.926752942422702,0.0917219806097098,-8.51645 +42,CSc1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-8.783396978154208,0.08654562379484741,-8.4668 +24,Cn1ccc2ccc(-c3cc(Nc4ccccc4C#N)cc4nccnc34)cc21,-8.62940366223464,0.07279448316920095,-8.86991 +29,Cn1ccc2ccc(-c3cc(Nc4ccccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.845187343575478,0.046881509293656504,-9.64602 +26,Cn1ccc2ccc(-c3cc(Nc4ccccc4C(N)=O)cc4nccnc34)cc21,-8.455589217995703,0.07041599137171128,-9.16944 +37,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(=O)NC4CCOCC4)cc4nccnc34)cc21,-10.666269742599436,0.08506885215947267,-9.99707 +36,CN(c1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1)c1cnccc1S(C)(=O)=O,-10.470083742469672,0.052076753235436785,-7.44054 +55,Cn1ccc2c(F)cc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-10.293034826993443,0.04793840935997357,-10.6355 +57,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ccn(C(F)F)c3c2)c2nccnc2c1,-10.17519720357378,0.062410312999104114,-10.4744 +60_adjust,CC1(C)COc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.481444543426996,0.06330757283016683,-8.14374 +30_flip_b,COc1ncccc1Nc1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1,-8.359954767146375,0.07342291889865957,-9.19819 +31,COc1ccncc1Nc1cc(-c2ccc3ccn(C)c3c2)c2nccnc2c1,-10.528684376311645,0.07459130937468816,-9.28247 +34,Cn1ccc2ccc(-c3cc(Nc4cnccc4C(N)=O)cc4nccnc34)cc21,-10.264937707144002,0.0824839544493099,-9.97238 +35,Cn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-9.307162840219124,0.04391011295820072,-10.1388 +52,CCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.847750813378866,0.0553932976599879,-10.3953 +53,CCCn1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-8.692087179747448,0.06143466958097232,-6.99764 +70,Cc1coc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-10.861617395714202,0.05473870419501538,-10.3039 +38,CN(C)c1cccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)c1,-8.83922638505316,0.06391408531639728,-8.75876 +69,Cc1csc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc12,-10.978082479212443,0.03725241968975575,-10.7146 +41,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(OC(F)(F)F)c2)c2nccnc2c1,-8.963652224576553,0.09301063343859808,-7.38769 +43,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(Br)c2)c2nccnc2c1,-8.901771327735831,0.08163630960556181,-7.997660000000001 +44,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(Br)cc2)c2nccnc2c1,-7.993466857809709,0.06179466490803588,-9.94868 +46,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(C(F)(F)F)cc2)c2nccnc2c1,-6.498218298353041,0.06150561422145284,-7.859360000000001 +63,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nsnc3c2)c2nccnc2c1,-8.339353306213468,0.05837072781686698,-8.56164 +47,CCc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-5.955646381310608,0.0752494972793027,-8.33345 +64,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3ncsc3c2)c2nccnc2c1,-7.811714080612294,0.061833567085214196,-9.42228 +48,COc1ccc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc1,-6.8494505454559,0.06899803650595035,-8.00636 +49,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc(N)cc2)c2nccnc2c1,-6.786297598223919,0.07801583178207241,-7.93429 +62_flip,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3nonc3c2)c2nccnc2c1,-8.510584193166972,0.07877626370309937,-7.691739999999999 +54,CC(C)n1ccc2ccc(-c3cc(Nc4cnccc4S(C)(=O)=O)cc4nccnc34)cc21,-7.84605223221562,0.0661761009796826,-8.17959 +56,Cc1cc(-c2cc(Nc3cnccc3S(C)(=O)=O)cc3nccnc23)cc2c1ccn2C,-10.444402938372418,0.05032934445452241,-10.5657 +58,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)CCO3)c2nccnc2c1,-9.425156656016874,0.06922402592531923,-9.13315 +39,CS(=O)(=O)c1ccncc1Nc1cc(-c2cccc(N)c2)c2nccnc2c1,-7.159170428336658,0.05561139803801301,-7.1975 +59,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3c(c2)OCCO3)c2nccnc2c1,-8.899473290088945,0.076849617511645,-8.11517 +65,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3scnc3c2)c2nccnc2c1,-9.664045504158107,0.046997643900167065,-9.4879 +67,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)nc3c2)c2nccnc2c1,-11.737369887085379,0.05747994951889456,-10.2436 +68,CS(=O)(=O)c1ccncc1Nc1cc(-c2ccc3sc(N)cc3c2)c2nccnc2c1,-10.415870862716234,0.05656917243395446,-9.77823 diff --git a/summaries/2026_mar_25/merck/shp2/README.md b/summaries/2026_mar_25/merck/shp2/README.md new file mode 100644 index 0000000..31615f9 --- /dev/null +++ b/summaries/2026_mar_25/merck/shp2/README.md @@ -0,0 +1,39 @@ +# Shp2 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.61 +- RMSE: 2.06 +- R²: 0.16 +- Kendall 𝜏: 0.18 +- Spearman ρ: 0.28 + +## System Details +- Ligands: 26 +- Host Atoms: 8422 +- Map Details: + - Edges: 46 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 27 + - Mean Dummy Atoms: 7.8 + - Median Dummy Atoms: 6.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 56.72 Hours +- Average Time Per Edge: 1.23 Hours +- Total Nanoseconds Simulated: 5048.20 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/merck/shp2/ddg_results.csv b/summaries/2026_mar_25/merck/shp2/ddg_results.csv new file mode 100644 index 0000000..d5b70b8 --- /dev/null +++ b/summaries/2026_mar_25/merck/shp2/ddg_results.csv @@ -0,0 +1,47 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +10,Example 23,-10.121216633513896,0.05651266284121899,-10.335065611221351,0.0558232180343673,-1.5860599999999998,0.21384897770745515,0.07943495913713183,-0.015463158571174418,0.06628030070383037 +10,Example 30,-43.53088774355876,0.05150104749170667,-41.24983539648734,0.05272277691786747,-2.00282,-2.281052347071413,0.07370243617869253,-2.0331039969075118,0.06034303416667212 +11,10,3.0805851095176364,0.0521500161238368,4.917994426108026,0.052553815549666524,-0.8001899999999997,-1.8374093165903904,0.07403733997480466,-1.7864098208782622,0.061716693594343126 +11,Example 30,-39.88777846478549,0.053832946190010736,-36.16511559521131,0.05465970733899816,-2.8030099999999996,-3.722662869574177,0.07671811847198497,-3.819513817785774,0.05661048083815496 +3,6,-12.048390737836838,0.07184388597813986,-11.631076127349564,0.06926187165364765,-2.5671,-0.41731461048727453,0.09979354096035636,-0.08923505850964464,0.09639214903889598 +3,Example 27,65.38629363035598,0.055509723353174036,66.09433390217612,0.05352423412570813,-3.0555900000000005,-0.7080402718201387,0.07711143252131641,0.29616347297536816,0.11196465076896342 +4,3,0.9294557502210299,0.042856654678212855,0.3740204456491893,0.04135285172269729,0.3591300000000004,0.5554353045718406,0.05955460683949624,0.8564111292630816,0.1123445938527524 +4,Example 27,68.51135829020603,0.06112717820404063,66.39119184035502,0.058563763557023404,-2.69646,2.1201664498510118,0.08465368460469681,1.1525746022384498,0.11293918416865699 +4,SHP836-2,1.286241901954477,0.05140643025532954,-0.12469904100938299,0.04973515004285941,-0.89114,1.41094094296386,0.07152766053340343,1.667575746049775,0.10572263933758594 +7,6,-25.58076385389779,0.05558729843102617,-26.136921424077666,0.05256466233292161,-0.95357,0.5561575701798791,0.07650484607548748,0.7226022108171177,0.08315567367251858 +Example 14,6,-56.694807923772345,0.07845265830249092,-63.60126658556222,0.07821169759926011,1.748190000000001,6.906458661789873,0.1107785594602381,6.46131455481916,0.09228508989371875 +Example 14,Example 27,17.22631896649914,0.08013779427072419,9.956661609404103,0.07789932762810055,1.2597000000000005,7.269657357095036,0.11176032979321,6.846713086304173,0.10844894855262985 +Example 14,Example 9,-0.10982104291411199,0.07892527436247355,0.592349248498908,0.07818112852095892,0.9841300000000004,-0.70217029141302,0.11109224900956151,0.16340122107445154,0.09452543543625715 +Example 1,6,-6.875008278393602,0.057368196122665104,-6.265701206388492,0.053806492605459146,0.9581400000000002,-0.6093070720051098,0.07865270861750343,-0.3513555298522979,0.06667224436079841 +Example 1,7,19.191335787168377,0.070867043031317,19.900206966030996,0.06424169674148507,1.9117100000000002,-0.7088711788626167,0.09565110238898175,-1.0739577406694156,0.07196730444053713 +Example 1,Example 3,-6.692617236416595,0.0668814657523245,-5.707193059820594,0.06310975583299532,0.7723099999999992,-0.9854241765960003,0.09195635781434387,-0.9629904630429298,0.06329026028071591 +Example 1,Example 4,-6.104329230093857,0.0677269872673743,-5.643156971210476,0.0628951845900557,0.7870899999999992,-0.46117225888338065,0.09242699307524974,-0.7448609962654462,0.06748305220094604 +Example 1,Example 5,4.292735867711142,0.052403130390937275,2.159312287012302,0.049422774249021584,1.42509,2.13342358069884,0.07203262239596255,1.6908504259600905,0.0622298823102729 +Example 1,Example 8,59.28921150837766,0.06172807240003855,65.55949164936541,0.06163343845716219,-0.7241499999999998,-6.2702801409877456,0.08722978653119129,-6.289380386870372,0.05745857292823232 +Example 22,Example 24,0.6052658979730328,0.04466011473236913,-0.5656978474581615,0.046376295565316784,0.1616099999999996,1.1709637454311943,0.064383900458655,1.3476682517437801,0.08693387127185388 +Example 22,Example 26,-0.2498505295952606,0.0531388723388022,-0.7915827804364801,0.052263645194904375,0.2797800000000006,0.5417322508412196,0.07453340433992243,0.23650346024424707,0.08766000679020429 +Example 22,Example 6,-73.50473121097157,0.06324572338932817,-73.92515365379015,0.05786916808465943,0.16957000000000022,0.4204224428185706,0.08572550461706235,0.510935469911975,0.08663671136812465 +Example 24,Example 23,0.23892198799735814,0.04364363818580476,1.8569240872227541,0.0415984690664677,0.33688000000000073,-1.618002099225396,0.06029261797904704,-1.8344561806951463,0.07607122492474512 +Example 24,Example 25,1.4329309563461803,0.039161468444055894,1.4715223913513098,0.03963655848607379,0.20730999999999966,-0.03859143500512961,0.05571963190218268,0.27861886783740974,0.08316732937584248 +Example 25,Example 23,-1.8357817315393643,0.048104936557825356,0.421531934754712,0.04642844756173202,0.12957000000000107,-2.2573136662940763,0.06685570779092016,-2.113075048532556,0.07530368142931645 +Example 26,Example 23,1.1185980279606111,0.05341896441376213,1.9213071224833158,0.049559878390088734,0.21870999999999974,-0.8027090945227047,0.07286815014174004,-0.7232913891956132,0.07690000050519222 +Example 26,Example 25,0.3237737198089435,0.06015798917353602,-1.5822706144379888,0.06137246638614012,0.08913999999999866,1.9060443342469324,0.08593930004207143,1.3897836593369428,0.08392605966955242 +Example 29,Example 28,10.827210666879745,0.07629104269708183,11.388739086122984,0.07646377455028949,-0.8345700000000003,-0.5615284192432378,0.10801403619106852,-0.5750329421196074,0.09451975800308424 +Example 29,Example 30,-37.33478425900161,0.07067248428510678,-35.09749311887334,0.0694895024793184,-1.5343200000000001,-2.237291140128271,0.09911302129312707,-1.9366707071597595,0.0764776679878091 +Example 2,Example 1,-1.8644579258723812,0.03820514702411692,-1.1161202893781004,0.03499727705939557,-0.7119599999999995,-0.7483376364942808,0.051811607393580116,-1.0612559048204906,0.05842083819040698 +Example 2,Example 30,32.314996080644484,0.047727442362675086,36.839050664531186,0.04615009412659035,-0.8808799999999994,-4.524054583886704,0.0663908121834311,-4.060389684929198,0.059805734265520445 +Example 2,Example 4,-8.212192869934828,0.07488902812191518,-6.283115817533896,0.07212693713785195,0.0751299999999997,-1.9290770524009329,0.10397433141854123,-1.8061169010859368,0.07250752827543323 +Example 30,Example 23,32.890754200880664,0.04993542269548597,31.104248472594186,0.04750404263690137,0.41676,1.786505728286475,0.06892155328070745,2.0176408383363373,0.061553834437013365 +Example 30,Example 3,-41.73997994126521,0.06713217716052546,-43.61072397109869,0.0641582408131258,0.9412299999999991,1.870744029833485,0.09286015870408157,2.0361433170657772,0.06457080270965429 +Example 30,Example 5,-31.69081619342464,0.05770361758105149,-35.758269187306745,0.055483831514026805,1.59401,4.067452993882106,0.08005100275085346,4.6899842060687975,0.06353180123779545 +Example 4,Example 3,-0.5135085223497844,0.03579428113741839,-0.3495649522888142,0.03464783218576891,-0.014780000000000015,-0.1639435700609702,0.049816692356254945,-0.21812946677748357,0.07648532125933578 +Example 6,Example 28,94.3619238082967,0.07641901696203586,96.29447084835553,0.07547907211120598,0.61191,-1.9325470400588318,0.10741022521255861,-1.6537264721595264,0.08982542795379082 +Example 6,Example 5,10.179820396356945,0.04557071233898042,8.45926566652897,0.04241857136587314,1.50617,1.7205547298279757,0.06225773060274342,1.674619968869119,0.07734771023464841 +Example 9,7,-36.897717671289044,0.06375223749599956,-41.92251684605323,0.06317407682321177,1.7176300000000007,5.024799174764184,0.08975138867010023,5.575311122927591,0.08563519248330483 +Example 9,Example 8,4.774441089956218,0.05270924022562992,4.42367386064912,0.048032512098768576,-0.9182299999999994,0.3507672293070979,0.07131189398467491,0.3598884767266348,0.0738619041601603 +SHP099-1 Example 7,11,12.464319799525594,0.04856480691854524,9.473805257689383,0.04772162291354487,3.398559999999999,2.990514541836211,0.0680873979862511,2.957360950281487,0.06350230296792864 +SHP099-1 Example 7,Example 28,22.444601286667318,0.07486525710572633,21.702667780329836,0.07022682792233706,1.2952999999999992,0.7419335063374812,0.1026480106068308,0.499484897535865,0.0833668095740791 +SHP099-1 Example 7,Example 29,9.41851829574199,0.0694710735172156,8.622158026253258,0.0679738699883273,2.1298699999999995,0.7963602694887331,0.09719401759791803,1.0745178396554724,0.08171064583245594 +SHP099-1 Example 7,Example 8,-3.0875206647945586,0.05858975897134657,1.0697239457941141,0.05769441543323009,0.04031999999999947,-4.157244610588673,0.08222776555703447,-4.152399474265952,0.06552110393316654 +SHP836-2,3,-0.7155610389763968,0.04342327192746079,0.5192892732104383,0.04167370847550517,1.2502700000000004,-1.234850312186835,0.060185368014057994,-0.8111646167866935,0.10468094463482544 +SHP836-2,6,-11.522805037581005,0.07023365804320304,-11.233454708134952,0.06491478471240307,-1.3168299999999995,-0.28935032944605255,0.09563836048567133,-0.9003996752963381,0.08858563708018426 diff --git a/summaries/2026_mar_25/merck/shp2/dg_comparison_plot.png b/summaries/2026_mar_25/merck/shp2/dg_comparison_plot.png new file mode 100644 index 0000000..3106179 Binary files /dev/null and b/summaries/2026_mar_25/merck/shp2/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/merck/shp2/dg_plot.png b/summaries/2026_mar_25/merck/shp2/dg_plot.png new file mode 100644 index 0000000..45c9011 Binary files /dev/null and b/summaries/2026_mar_25/merck/shp2/dg_plot.png differ diff --git a/summaries/2026_mar_25/merck/shp2/dg_results.csv b/summaries/2026_mar_25/merck/shp2/dg_results.csv new file mode 100644 index 0000000..2e27c38 --- /dev/null +++ b/summaries/2026_mar_25/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,-8.079873633596929,0.04607323246707942,-7.15428 +Example 23,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Cl)CC1,-8.095336792168103,0.04764803785492783,-8.74034 +Example 30,CC1([NH3+])CCN(c2nnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-10.11297763050444,0.03896843623337505,-9.1571 +11,CNc1nc(N2CCC(C)([NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-6.293463812718667,0.041063457212617796,-6.35409 +3,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-7.375964321738387,0.078746845870403,-5.46294 +6,Nc1nc(N2CCC([NH3+])CC2)ncc1-c1cccc(Cl)c1Cl,-7.465199380248031,0.05559119230417468,-8.03004 +Example 27,C[C@@H]1CN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-7.079800848763019,0.0795928218326184,-8.51853 +4,C[C@@H]1CN(c2ncc(-c3ccc(Cl)c(Cl)c3)c(N)n2)C[C@H](C)[NH2+]1,-8.232375451001468,0.08012641283249168,-5.82207 +SHP836-2,C[C@@H]1CN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)C[C@H](C)[NH2+]1,-6.564799704951693,0.06897125803624568,-6.71321 +7,C[NH+](C)C1CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-8.18780159106515,0.061842423967133346,-7.07647 +Example 14,Nc1nc(N2CC[C@@H](C[NH3+])C2)cnc1-c1cccc(Cl)c1Cl,-13.926513935067192,0.07366245417369706,-9.77823 +Example 9,Nc1nc(N2CCC(C[NH3+])CC2)cnc1-c1cccc(Cl)c1Cl,-13.76311271399274,0.059235975466957566,-8.7941 +Example 1,CC1([NH3+])CCN(c2ncc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-7.1138438503957335,0.03680770987587092,-8.98818 +Example 3,CC1([NH3+])CCN(c2ncc(-c3ccc(Cl)s3)c(N)n2)CC1,-8.076834313438663,0.05148640150655784,-8.21587 +Example 4,Cc1ccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)s1,-7.85870484666118,0.05656107166637953,-8.20109 +Example 5,COc1cc(Cl)c(Cl)c(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1,-5.422993424435643,0.050177193485129584,-7.56309 +Example 8,CC1(C[NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-13.403224237266105,0.0441211978151399,-9.71233 +Example 22,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2Br)CC1,-7.608548863216737,0.06356887779554342,-9.23883 +Example 24,Cc1nc(-c2cccc(Cl)c2Cl)c(N)nc1N1CCC(C)([NH3+])CC1,-6.260880611472957,0.059300048483340445,-9.07722 +Example 26,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C(N)=O)CC1,-7.37204540297249,0.06035954411916916,-8.95905 +Example 6,CC1([NH3+])CCN(c2ncc(-c3cc(O)cc(Cl)c3Cl)c(N)n2)CC1,-7.097613393304762,0.05886355011803998,-9.06926 +Example 25,CC1([NH3+])CCN(c2nc(N)c(-c3cccc(Cl)c3Cl)nc2C#N)CC1,-5.982261743635547,0.058312167901591036,-8.86991 +Example 29,CC1([NH3+])CCN(c2cnc(C3=CCCCC3)c(N)n2)CC1,-8.176306923344681,0.06580497457167614,-7.62278 +Example 28,CC1([NH3+])CCN(c2cnc(-c3cccc4cc[nH]c34)c(N)n2)CC1,-8.751339865464288,0.06785049723165382,-8.45735 +Example 2,Cc1cccc(-c2cnc(N3CCC(C)([NH3+])CC3)nc2N)c1Cl,-6.052587945575243,0.04536724400449546,-8.27622 +SHP099-1 Example 7,CC1([NH3+])CCN(c2cnc(-c3cccc(Cl)c3Cl)c(N)n2)CC1,-9.250824763000153,0.04843898186355805,-9.75265 diff --git a/summaries/2026_mar_25/miscellaneous_set/cdk8/README.md b/summaries/2026_mar_25/miscellaneous_set/cdk8/README.md new file mode 100644 index 0000000..51fae1e --- /dev/null +++ b/summaries/2026_mar_25/miscellaneous_set/cdk8/README.md @@ -0,0 +1,39 @@ +# Cdk8 Map + +![Retrospective dG performance](dg_plot.png) + +## Statistics Summary +- MUE: 1.05 +- RMSE: 1.26 +- R²: 0.04 +- Kendall 𝜏: 0.11 +- Spearman ρ: 0.14 + +## System Details +- Ligands: 10 +- Host Atoms: 11038 +- Map Details: + - Edges: 16 + - Min Dummy Atoms: 1 + - Max Dummy Atoms: 9 + - Mean Dummy Atoms: 4.9 + - Median Dummy Atoms: 5.0 + +## Simulation Details +- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e) +- GPU: RTX 4090 +- MPS Processes: 12 +- Total Wallclock Time: 4.82 Hours +- Average Time Per Edge: 0.30 Hours +- Total Nanoseconds Simulated: 1357.40 +- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py +- Ligand Charges: Amber AM1BCC ELF10 +- Simulation Details: + - Seed: 4115 + - 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/2026_mar_25/miscellaneous_set/cdk8/ddg_results.csv b/summaries/2026_mar_25/miscellaneous_set/cdk8/ddg_results.csv new file mode 100644 index 0000000..8606ba6 --- /dev/null +++ b/summaries/2026_mar_25/miscellaneous_set/cdk8/ddg_results.csv @@ -0,0 +1,17 @@ +mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol) +12,14,-4.362888919888917,0.039587535042645346,-4.574186530904492,0.0403271961099941,-1.1986399999999993,0.2112976110155749,0.05651066869934028,0.49760932983313744,0.04968811541890736 +12,15,6.254281968523332,0.04470857912145455,5.795350929451949,0.04589672792403101,0.11278000000000077,0.4589310390713838,0.06407313540940454,0.05256173821059562,0.058075525191155164 +12,22,-6.060136030024535,0.05000903022215478,-5.250319951414397,0.04982146111933164,-1.4571400000000008,-0.809816078610138,0.07059094199559504,-0.763328265183981,0.05494237669427671 +13,19,15.711684994759425,0.04566563124850616,15.88458200079157,0.0458601468752172,0.9724000000000004,-0.17289700603214428,0.06471864452181485,-0.24285491857462027,0.058215559345571 +13,20,19.16902677499363,0.05135289393374469,19.066229349442665,0.048763914567291365,0.9141000000000012,0.10279742555096351,0.07081694062367086,0.2022239269249635,0.06288663105861439 +13,21,24.391717272673983,0.05089716139183739,22.309366853427136,0.049050343974432635,1.3348600000000008,2.0823504192468474,0.07068562287875026,2.0667449764359898,0.06184927581447772 +14,17,10.444782994592032,0.04655156739011897,7.664941953065567,0.043037702810759464,0.6362999999999985,2.779841041526465,0.06339788868490842,2.868464317567172,0.057692712514733784 +14,19,7.700612721714846,0.049450435638686736,8.646406327949313,0.048972743639261546,0.8067999999999991,-0.9457936062344673,0.0695965171859392,-0.8237539266395988,0.048512365343795924 +14,20,12.931566403257586,0.04681696630826138,13.494253389442527,0.046335609326750786,0.7484999999999999,-0.5626869861849407,0.06586969732730033,-0.378675081140015,0.05402894231089959 +15,21,30.784384713189752,0.06043853394621232,28.814149282361896,0.06060861005330857,-0.1421600000000005,1.9702354308278527,0.0855933408517361,1.930893559993553,0.06077490413364228 +15,22,-11.058902127526478,0.054929162850359294,-10.830336103235064,0.057066785244561324,-1.5699200000000015,-0.22856602429141384,0.07920751801180348,-0.8158900033945766,0.05796491290290696 +16,17,27.996536473288398,0.05537689604466922,27.266964227467952,0.05367410947375224,0.24019999999999975,0.7295722458204447,0.07712010531205492,1.3403337493785443,0.06546245024112549 +16,20,9.732766301099671,0.056254798035333474,11.255520683593009,0.05482933106419427,0.35240000000000116,-1.522754382493337,0.07855480791742271,-1.9068056493286427,0.062257609346156435 +16,22,-5.325553291760988,0.0587506755958797,-2.7925040977962885,0.05363525667067561,-0.6546000000000003,-2.5330491939646995,0.07955113224273774,-2.789068163205746,0.058420515486940536 +17,22,-12.925649519020977,0.05809929251300091,-8.019110209132524,0.0534271328914379,-0.8948,-4.906539309888453,0.07893026238085497,-4.1294019125842905,0.06227523601112132 +19,21,10.259917928334234,0.0463927898177951,7.986093092121184,0.045385616220987454,0.36246000000000045,2.2738248362130493,0.0649010408763748,2.30959989501061,0.05689343880268526 diff --git a/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_comparison_plot.png b/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_comparison_plot.png new file mode 100644 index 0000000..7637577 Binary files /dev/null and b/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_comparison_plot.png differ diff --git a/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_plot.png b/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_plot.png new file mode 100644 index 0000000..8134e9c Binary files /dev/null and b/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_plot.png differ diff --git a/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_results.csv b/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_results.csv new file mode 100644 index 0000000..b2ef463 --- /dev/null +++ b/summaries/2026_mar_25/miscellaneous_set/cdk8/dg_results.csv @@ -0,0 +1,11 @@ +mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol) +12,COC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.134469162014078,0.03893263576488695,-9.83296 +14,CNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-10.63685983218094,0.030873268150315807,-11.0316 +15,CN(C)C(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.081907423803482,0.04309311428322562,-9.72018 +22,CNC(=O)c1cc2c(Oc3ccc(I)cc3)cncc2s1,-11.897797427198059,0.038767442902704397,-11.2901 +13,NC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.217758840245919,0.04459552045832711,-11.1972 +19,CC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.46061375882054,0.03742046104698107,-10.2248 +20,CCC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-11.015534913320955,0.044339236810676065,-10.2831 +21,O=C(c1cc2c(Oc3ccc(Cl)cc3)cncc2s1)C1CC1,-9.15101386380993,0.04285525024808823,-9.86234 +17,O=C(NC1CC1)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-7.768395514613768,0.04873695098204663,-10.3953 +16,CCNC(=O)c1cc2c(Oc3ccc(Cl)cc3)cncc2s1,-9.108729263992313,0.043704027280622705,-10.6355