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ParDOCK DATA SET

The 226 protein-ligand complexes uploaded here have been prepared in the force field compatible manner. Experimental binding free energies in kcal/mol (EBFE), Predicted binding free energies in kcal/mol (PBFE), Root Mean Square Deviation(RMSD) in Å, name of the protein and the ligand charge of each complex are provided. Click on the PDB ID to download the protein-ligand complex.

S.No.PDBIDNameLigand ChargeEBFEPBFERMSD
11a30HIV-1 Protease-2-5.84-6.221.034
21a4kAntibody FAB-1-6.79-8.10.631
31a4qNeuraminidase-1-11.77-8.990.346
41a4wAlpha Thrombin1-8.13-9.810.44
51a9mHIV-1 Protease1-9.41-11.320.7
61aaqHIV-1 Protease1-11.45-11.210.271
71ac4Cytochrome C0-3.85-3.920.573
81acjAcetyl choline esterase0-10.08-4.550.158
91acmAspartate carbamoyltransferase-5-10.31-7.543.103
101acoAconitase3-5.17-8.321.178
111ae8Alpha Thrombin1-8.99-8.260.373
121aebCytochrome C0-4.81-3.462.936
131aeeCytochrome C0-3.96-3.091.412
141ai4Pencillin acylase-1-3.46-4.090.486
151ai5Pencillin acylase-1-5.14-4.570.165
161ai6Pencillin acylase-1-5.46-4.810.138
171ajnPencillin acylase-1-3.64-4.320.269
181ajpPencillin acylase-1-3.08-3.990.522
191ajvHIV-1 Protease0-10.59-10.940.21
201ajxHIV-1 Protease0-10.86-10.260.434
211apbL-arabinose - binding protein0-7.94-4.340.367
221aptPenicillopepsin1-12.82-11.430.392
231apuPenicillopepsin0-10.5-11.210.969
241apvPenicillopepsin0-12.35-11.770.569
251apwPenicillopepsin0-10.98-9.610.42
261b38Protein-Kinase2-4-9.4-10.670.361
271b39Protein-Kinase2-4-8.97-9.870.334
281b5gThrombin1-10.91-10.50.297
291b6jHIV-1 Protease1-10.76-12.60.371
301b6kHIV-1 Protease1-11.88-13.020.313
311b6lHIV-1 Protease1-11.28-11.760.382
321b6mHIV-1 Protease1-11.41-11.840.494
331b9sNeuraminidase-1-4.39-6.253.11
341b9tNeuraminidase0-7.04-8.150.243
351b9vNeuraminidase-1-5.04-9.050.243
361ba8Thrombin1-12.27-10.260.567
371bb0Thrombin1-11.4-10.20.465
381bdrHIV-1 Protease0-9.07-10.840.306
391bilRenin0-12.64-13.790.308
401bimRenin0-12.12-14.020.177
411bmaElastase1-6.33-9.980.629
421bmmAlpha Thrombin1-9.75-10.060.337
431bmnAlpha Thrombin1-11.58-8.681.592
441braTrypsin1-2.5-4.922.876
451bv7HIV-1 Protease0-12.64-14.980.121
461bv9HIV-1 Protease0-12.17-15.080.788
471bwaHIV-1 Protease0-10.33-14.140.366
481bwbHIV-1 Protease0-10.08-14.820.439
491c29Tryptophan synthase0-8.74-7.370.215
501c2tGlycinamide Ribonucleotide Transformaylase1-11.07-11.230.29
511c5cDecarboxylase Antibody 21D8-2-9.49-7.780.408
521c83Tyrosine Phosphatase 1B0-6.59-7.460.225
531c85Tyrosine Phosphatase-2-6.41-8.20.957
541c86Tyrosine Phosphatase-2-7.09-8.240.404
551c87Tyrosine Phosphatase 1B-2-6.59-8.520.185
561c88Tyrosine Phosphatase 1B-1-8.86-8.80.159
571c8kGlycogen Phosphorylase1-6.79-7.820.522
581c9dTryptophan synthase-2-8.71-10.190.123
591cbsCellular Retinoic Acid Binding Protein Type II-1-9.82-7.540.496
601cdgCyclodextrin glycosyltransferase0-3.3-2.440.331
611cf8Catalytic Antibody 19A4-1-8.23-8.320.292
621comChorismate Mutase-2-5.44-6.220.446
631cpiHIV-1 Protease0-10.07-13.140.32
641cqpAntigen CD11A0-6.61-6.640.324
651cscCitrate synthase-5-9.81-12.040.48
661ctrCalmodulin0-5.84-5.460.332
671cttCytidine deaminase0-6.24-3.930.164
681cvuCyclooxygenase 2-1-10.76-6.940.318
691cw2Tyrosine Phosphatase-2-8.49-8.120.118
701cx2Cyclooxygenase 20-10.94-7.160.241
711cx9Tryptophan synthase-2-9.32-8.540.458
721d3dAlpha thrombin0-12.55-10.780.406
731d3hDihydroorate Dehydrogenase0-6.01-7.460.263
741d3tAlpha thrombin0-7.78-9.911.006
751d4lHIV-1 Protease0-11.92-12.480.322
761d4pAlpha Thrombin1-8.59-8.940.402
771dg5Dihydrofolate Reductase0-5.53-6.750.241
781dhfDihydrofolate Reductase-2-10.09-8.771.396
791dieD - Xylose isomerase0-2.92-2.780.16
801dmpHIV-1 Protease0-13.03-11.920.344
811dogGlycoamylase 4710-5.48-3.230.318
821dr1Dihydrofolate Reductase1-7.59-5.290.318
831drfDihydrofolate Reductase-2-10.15-9.20.234
841dwbAlpha Thrombin1-3.98-5.060.582
851dwcAlpha Thrombin0-10.1-8.540.274
861dwdAlpha Thrombin1-11.14-10.40.483
871dy9Protease / Helicase NS3 (P70)-2-10.32-10.290.184
881c85Tyrosine Phosphatase-2-6.41-8.20.957
891eedEndothiapepsin-1-6.54-8.490.818
901elaElastase1-8.66-8.540.432
911elbElastase0-9.75-7.190.316
921eldElastase0-9.13-8.630.187
931eleElastase0-9.33-8.760.848
941entEndothiapepsin-1-9.55-80.878
951enut-RNA guanine transglycosylase0-7.02-6.020.552
961epoEndothiapepsin0-10.86-9.950.729
971eppEndothiapepsin1-9.77-10.190.27
981etsEpsilon Thrombin1-11.62-9.770.682
991ettEpsilon Thrombin1-8.44-8.880.374
1001ezqHuman coagulation factor XA1-12.5-11.241.035
1011f0rHuman coagulation factor XA0-10.58-8.80.545
1021f0tTrypsin1-8.29-6.922.363
1031f0uTrypsin1-9.89-8.981.599
1041f3et-RNA guanine transglycosylase0-9.25-6.520.104
1051faxHuman coagulation factor XA0-10.07-10.60.521
1061fkgFK506 Binding Protein0-8.81-6.570.256
1071flrFAB Fragment-1-6.35-6.250.183
1081g2kHIV-1 Protease0-10.81-12.130.37
1091ghbGamma chymotrypsin-1-1.71-6.130.256
1101gnoHIV-1 Protease1-10.57-10.10.29
1111gpyGlycogen Phosphorylase-2-6.4-7.070.362
1121hbvHIV-1 Protease0-8.68-10.910.442
1131hdc3 - alpha 20 - beta - hydroxysteroid dehydrogenase-2-8.17-8.030.821
1141hdtAlpha Thrombin1-10.6-11.870.272
1151hewLysozyme0-8.18-8.370.501
1161hgeHemagglutinin-1-3.09-4.490.799
1171hghHemagglutinin-1-3.89-4.70.204
1181hgiHemagglutinin-1-3.65-4.830.889
1191hgjHemagglutinin0-2.26-3.650.135
1201hihHIV-1 Protease0-10.97-11.80.204
1211hiiHIV-2 Protease0-9.89-11.790.276
1221hivHIV-1 Protease0-12.64-13.140.344
1231hosHIV-1 Protease-1-11.74-13.180.327
1241hpoHIV-1 Protease0-11.82-11.140.388
1251hpsHIV-1 Protease0-12.66-10.940.325
1261hpvHIV-1 Protease0-12.58-10.830.189
1271hpxHIV-1 Protease0-12.53-13.180.416
1281hriHuman Rhinovirus1-5.91-7.670.208
1291hrnRenin0-10.94-11.820.216
1301hsgHIV-1 Protease0-12.93-12.490.347
1311hshHIV-1 Protease1-11.69-12.070.332
1321hteHIV-1 Protease0-7.69-8.060.219
1331htfHIV-1 Protease0-11.04-9.990.253
1341htgHIV-1 Protease0-13.21-12.860.44
1351hvhHIV-1 Protease1-10.81-12.180.454
1361hviHIV-1 Protease0-13.74-15.920.208
1371hvjHIV-1 Protease0-14.26-15.020.206
1381hvkHIV-1 Protease0-13.8-15.480.523
1391hvlHIV-1 Protease0-12.28-14.880.319
1401hvrHIV-1 Protease0-12.97-12.960.195
1411hxbHIV-1 Protease1-13.48-12.760.287
1421hxwHIV-1 Protease0-14.54-14.60.327
1431idaHIV-2 Protease0-11.86-12.550.327
1441imbInositol monophosphatase-2-5.73-3.32.93
1451ivbNeuraminidase-1-4.14-5.391.882
1461ivfNeuraminidase-1-6.66-7.620.878
1471k1lTrypsin1-9.56-7.410.374
1481k1nTrypsin0-8.82-9.470.341
1491lybCathepsin D-1-15.57-12.360.219
1501mcbImmunoglobulin-1-6.6-8.50.396
1511mcfImmunoglobulin-1-7.02-8.540.472
1521mchImmunoglobulin-1-7.02-8.810.284
1531mcjImmunoglobulin0-5.16-5.920.381
1541mcsImmunoglobulin-1-6.6-8.20.277
1551mrkAlpha trichosanthin0-6.17-5.780.389
1561mtwTrypsin1-10.07-7.841.011
1571nisEnolase-2-4.08-6.660.188
1581nnbNeuraminidase-1-5.45-7.10.421
1591nscNeuraminidase-1-4.08-7.850.148
1601olaOligopeptide Binding Protein1-9.54-10.160.248
1611pdzEnolase-3-5.03-5.80.381
1621pgp6-Phosphogluconate Dehydrogenase-3-7.77-9.152.368
1631phhp-Hydroxybenzoate Hydroxylase-1-3.98-4.610.588
1641ppcTrypsin1-8.8-8.460.415
1651pphTrypsin1-8.48-6.351.454
1661ppkPenicillopepsin1-10.44-8.910.441
1671ppmPenicillopepsin-1-7.95-9.740.375
1681psopepsin-1-14.11-12.340.493
1691qbrHIV-1 Protease0-14.42-14.540.331
1701qbtHIV-1 Protease0-14.49-14.610.447
1711qbuHIV-1 Protease0-13.97-12.050.295
1721rbpRetinol Binding Protein0-9.17-7.780.233
1731rgkRibonuclease T1-2-5.87-6.820.225
1741rglRibonuclease T1-2-6.04-5.732.657
1751rneRenin0-11.94-15.10.45
1761sncStaphylococcal nuclease-4-9.25-11.890.228
1771sreStreptavidin-1-5.45-6.190.266
1781tlcThymidylate Synthase-2-10.98-10.080.392
1791tngTrypsin1-4-3.930.496
1801tnhTrypsin1-4.59-4.490.379
1811tniTrypsin1-2.32-3.740.534
1821tnjTrypsin1-2.67-3.720.316
1831tnkTrypsin1-2.03-3.810.361
1841tnlTrypsin1-2.56-3.561.411
1851tphTriose phosphate Isomerase-3-3.1-5.210.381
1861tppTrypsin0-7.95-6.050.212
1871ulbPurine Nucleoside Phosphorylase0-2.8-2.840.152
1881uvsAlpha Thrombin0-7.41-7.530.716
1892abhPhosphate Binding Protein-2-8.88-7.380.571
1902acsAldose Reductase-3-2.75-4.80.775
1912ak3Adenylate kinase-2-5.25-9.830.435
1922cgrIGG 2B Fab Fragment-1-9.93-10.560.175
1932cmdMalate Dehydrogenase-3-6.24-7.770.347
1942er7Endothiapepsin-1-12.27-13.641.034
1952gbpD - Galactose D . Glucose binding protein0-10.35-4.740.426
1962ifbIntestinal Fatty Acid Binding Protein-1-7.41-8.070.368
1972mcpImmunoglobulin-1-7.13-6.770.131
1982pk4Human plasminogen0-5.88-2.990.331
1992r04Rhinovirus 140-8.48-7.520.29
2002simSialidase-1-8.75-6.80.479
2012upjHIV-1 Protease0-10.14-10.70.493
2022weaPenicillopepsin-1-8.37-6.480.248
2032webPenicillopepsin-1-7.03-9.280.371
2042wecPenicillopepsin-1-6.8-6.750.468
2052ypiTriose Phosphate Isomerase-3-6.58-7.190.385
2063er3Endothiapepsin1-9.68-12.890.884
2073er5Endothiapepsin0-12.35-14.470.394
2083ptbTrypsin1-6.46-5.360.979
2094dfrDihydrofolate Reductase-1-13.23-11.40.301
2104er2Endothiapepsin-1-11.03-10.30.348
2114estElastase0-9.55-8.080.509
2124hmgHemagglutinin-1-3.48-3.970.328
2134phvHIV-1 Protease0-12.47-12.290.381
2144ts1Tyrosyl-T / RNA Synthetase0-7.64-4.810.199
2155cnaAgglutinin0-2.73-3.710.77
2165enlEnolase-3-5.24-6.591.05
2175hvpHIV-1 Protease-1-10.51-12.90.22
2185timTriose Phosphate Isomerase-2-3.14-3.090.543
2196enlEnolase-3-4.14-5.530.506
2206rntRibonuclease-2-8.67-7.260.315
2216timTriose phosphate isomerase-2-4.37-7.590.323
2227dfrDihydrofolate Reductase-2-10.09-10.730.292
2237gpbGlycogen Phosphorylase-2-7.53-7.640.943
2247timTriose phosphate isomerase-2-7.35-7.010.12
2258gpbGlycogen Phosphorylase-2-4.91-5.960.53
2269hvpHIV-1 Protease0-11.38-13.90.515