ParDOCK
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. | PDBID | Name | Ligand Charge | EBFE | PBFE | RMSD |
| 1 | 1a30 | HIV-1 Protease | -2 | -5.84 | -6.22 | 1.034 |
| 2 | 1a4k | Antibody FAB | -1 | -6.79 | -8.1 | 0.631 |
| 3 | 1a4q | Neuraminidase | -1 | -11.77 | -8.99 | 0.346 |
| 4 | 1a4w | Alpha Thrombin | 1 | -8.13 | -9.81 | 0.44 |
| 5 | 1a9m | HIV-1 Protease | 1 | -9.41 | -11.32 | 0.7 |
| 6 | 1aaq | HIV-1 Protease | 1 | -11.45 | -11.21 | 0.271 |
| 7 | 1ac4 | Cytochrome C | 0 | -3.85 | -3.92 | 0.573 |
| 8 | 1acj | Acetyl choline esterase | 0 | -10.08 | -4.55 | 0.158 |
| 9 | 1acm | Aspartate carbamoyltransferase | -5 | -10.31 | -7.54 | 3.103 |
| 10 | 1aco | Aconitase | 3 | -5.17 | -8.32 | 1.178 |
| 11 | 1ae8 | Alpha Thrombin | 1 | -8.99 | -8.26 | 0.373 |
| 12 | 1aeb | Cytochrome C | 0 | -4.81 | -3.46 | 2.936 |
| 13 | 1aee | Cytochrome C | 0 | -3.96 | -3.09 | 1.412 |
| 14 | 1ai4 | Pencillin acylase | -1 | -3.46 | -4.09 | 0.486 |
| 15 | 1ai5 | Pencillin acylase | -1 | -5.14 | -4.57 | 0.165 |
| 16 | 1ai6 | Pencillin acylase | -1 | -5.46 | -4.81 | 0.138 |
| 17 | 1ajn | Pencillin acylase | -1 | -3.64 | -4.32 | 0.269 |
| 18 | 1ajp | Pencillin acylase | -1 | -3.08 | -3.99 | 0.522 |
| 19 | 1ajv | HIV-1 Protease | 0 | -10.59 | -10.94 | 0.21 |
| 20 | 1ajx | HIV-1 Protease | 0 | -10.86 | -10.26 | 0.434 |
| 21 | 1apb | L-arabinose - binding protein | 0 | -7.94 | -4.34 | 0.367 |
| 22 | 1apt | Penicillopepsin | 1 | -12.82 | -11.43 | 0.392 |
| 23 | 1apu | Penicillopepsin | 0 | -10.5 | -11.21 | 0.969 |
| 24 | 1apv | Penicillopepsin | 0 | -12.35 | -11.77 | 0.569 |
| 25 | 1apw | Penicillopepsin | 0 | -10.98 | -9.61 | 0.42 |
| 26 | 1b38 | Protein-Kinase2 | -4 | -9.4 | -10.67 | 0.361 |
| 27 | 1b39 | Protein-Kinase2 | -4 | -8.97 | -9.87 | 0.334 |
| 28 | 1b5g | Thrombin | 1 | -10.91 | -10.5 | 0.297 |
| 29 | 1b6j | HIV-1 Protease | 1 | -10.76 | -12.6 | 0.371 |
| 30 | 1b6k | HIV-1 Protease | 1 | -11.88 | -13.02 | 0.313 |
| 31 | 1b6l | HIV-1 Protease | 1 | -11.28 | -11.76 | 0.382 |
| 32 | 1b6m | HIV-1 Protease | 1 | -11.41 | -11.84 | 0.494 |
| 33 | 1b9s | Neuraminidase | -1 | -4.39 | -6.25 | 3.11 |
| 34 | 1b9t | Neuraminidase | 0 | -7.04 | -8.15 | 0.243 |
| 35 | 1b9v | Neuraminidase | -1 | -5.04 | -9.05 | 0.243 |
| 36 | 1ba8 | Thrombin | 1 | -12.27 | -10.26 | 0.567 |
| 37 | 1bb0 | Thrombin | 1 | -11.4 | -10.2 | 0.465 |
| 38 | 1bdr | HIV-1 Protease | 0 | -9.07 | -10.84 | 0.306 |
| 39 | 1bil | Renin | 0 | -12.64 | -13.79 | 0.308 |
| 40 | 1bim | Renin | 0 | -12.12 | -14.02 | 0.177 |
| 41 | 1bma | Elastase | 1 | -6.33 | -9.98 | 0.629 |
| 42 | 1bmm | Alpha Thrombin | 1 | -9.75 | -10.06 | 0.337 |
| 43 | 1bmn | Alpha Thrombin | 1 | -11.58 | -8.68 | 1.592 |
| 44 | 1bra | Trypsin | 1 | -2.5 | -4.92 | 2.876 |
| 45 | 1bv7 | HIV-1 Protease | 0 | -12.64 | -14.98 | 0.121 |
| 46 | 1bv9 | HIV-1 Protease | 0 | -12.17 | -15.08 | 0.788 |
| 47 | 1bwa | HIV-1 Protease | 0 | -10.33 | -14.14 | 0.366 |
| 48 | 1bwb | HIV-1 Protease | 0 | -10.08 | -14.82 | 0.439 |
| 49 | 1c29 | Tryptophan synthase | 0 | -8.74 | -7.37 | 0.215 |
| 50 | 1c2t | Glycinamide Ribonucleotide Transformaylase | 1 | -11.07 | -11.23 | 0.29 |
| 51 | 1c5c | Decarboxylase Antibody 21D8 | -2 | -9.49 | -7.78 | 0.408 |
| 52 | 1c83 | Tyrosine Phosphatase 1B | 0 | -6.59 | -7.46 | 0.225 |
| 53 | 1c85 | Tyrosine Phosphatase | -2 | -6.41 | -8.2 | 0.957 |
| 54 | 1c86 | Tyrosine Phosphatase | -2 | -7.09 | -8.24 | 0.404 |
| 55 | 1c87 | Tyrosine Phosphatase 1B | -2 | -6.59 | -8.52 | 0.185 |
| 56 | 1c88 | Tyrosine Phosphatase 1B | -1 | -8.86 | -8.8 | 0.159 |
| 57 | 1c8k | Glycogen Phosphorylase | 1 | -6.79 | -7.82 | 0.522 |
| 58 | 1c9d | Tryptophan synthase | -2 | -8.71 | -10.19 | 0.123 |
| 59 | 1cbs | Cellular Retinoic Acid Binding Protein Type II | -1 | -9.82 | -7.54 | 0.496 |
| 60 | 1cdg | Cyclodextrin glycosyltransferase | 0 | -3.3 | -2.44 | 0.331 |
| 61 | 1cf8 | Catalytic Antibody 19A4 | -1 | -8.23 | -8.32 | 0.292 |
| 62 | 1com | Chorismate Mutase | -2 | -5.44 | -6.22 | 0.446 |
| 63 | 1cpi | HIV-1 Protease | 0 | -10.07 | -13.14 | 0.32 |
| 64 | 1cqp | Antigen CD11A | 0 | -6.61 | -6.64 | 0.324 |
| 65 | 1csc | Citrate synthase | -5 | -9.81 | -12.04 | 0.48 |
| 66 | 1ctr | Calmodulin | 0 | -5.84 | -5.46 | 0.332 |
| 67 | 1ctt | Cytidine deaminase | 0 | -6.24 | -3.93 | 0.164 |
| 68 | 1cvu | Cyclooxygenase 2 | -1 | -10.76 | -6.94 | 0.318 |
| 69 | 1cw2 | Tyrosine Phosphatase | -2 | -8.49 | -8.12 | 0.118 |
| 70 | 1cx2 | Cyclooxygenase 2 | 0 | -10.94 | -7.16 | 0.241 |
| 71 | 1cx9 | Tryptophan synthase | -2 | -9.32 | -8.54 | 0.458 |
| 72 | 1d3d | Alpha thrombin | 0 | -12.55 | -10.78 | 0.406 |
| 73 | 1d3h | Dihydroorate Dehydrogenase | 0 | -6.01 | -7.46 | 0.263 |
| 74 | 1d3t | Alpha thrombin | 0 | -7.78 | -9.91 | 1.006 |
| 75 | 1d4l | HIV-1 Protease | 0 | -11.92 | -12.48 | 0.322 |
| 76 | 1d4p | Alpha Thrombin | 1 | -8.59 | -8.94 | 0.402 |
| 77 | 1dg5 | Dihydrofolate Reductase | 0 | -5.53 | -6.75 | 0.241 |
| 78 | 1dhf | Dihydrofolate Reductase | -2 | -10.09 | -8.77 | 1.396 |
| 79 | 1die | D - Xylose isomerase | 0 | -2.92 | -2.78 | 0.16 |
| 80 | 1dmp | HIV-1 Protease | 0 | -13.03 | -11.92 | 0.344 |
| 81 | 1dog | Glycoamylase 471 | 0 | -5.48 | -3.23 | 0.318 |
| 82 | 1dr1 | Dihydrofolate Reductase | 1 | -7.59 | -5.29 | 0.318 |
| 83 | 1drf | Dihydrofolate Reductase | -2 | -10.15 | -9.2 | 0.234 |
| 84 | 1dwb | Alpha Thrombin | 1 | -3.98 | -5.06 | 0.582 |
| 85 | 1dwc | Alpha Thrombin | 0 | -10.1 | -8.54 | 0.274 |
| 86 | 1dwd | Alpha Thrombin | 1 | -11.14 | -10.4 | 0.483 |
| 87 | 1dy9 | Protease / Helicase NS3 (P70) | -2 | -10.32 | -10.29 | 0.184 |
| 88 | 1c85 | Tyrosine Phosphatase | -2 | -6.41 | -8.2 | 0.957 |
| 89 | 1eed | Endothiapepsin | -1 | -6.54 | -8.49 | 0.818 |
| 90 | 1ela | Elastase | 1 | -8.66 | -8.54 | 0.432 |
| 91 | 1elb | Elastase | 0 | -9.75 | -7.19 | 0.316 |
| 92 | 1eld | Elastase | 0 | -9.13 | -8.63 | 0.187 |
| 93 | 1ele | Elastase | 0 | -9.33 | -8.76 | 0.848 |
| 94 | 1ent | Endothiapepsin | -1 | -9.55 | -8 | 0.878 |
| 95 | 1enu | t-RNA guanine transglycosylase | 0 | -7.02 | -6.02 | 0.552 |
| 96 | 1epo | Endothiapepsin | 0 | -10.86 | -9.95 | 0.729 |
| 97 | 1epp | Endothiapepsin | 1 | -9.77 | -10.19 | 0.27 |
| 98 | 1ets | Epsilon Thrombin | 1 | -11.62 | -9.77 | 0.682 |
| 99 | 1ett | Epsilon Thrombin | 1 | -8.44 | -8.88 | 0.374 |
| 100 | 1ezq | Human coagulation factor XA | 1 | -12.5 | -11.24 | 1.035 |
| 101 | 1f0r | Human coagulation factor XA | 0 | -10.58 | -8.8 | 0.545 |
| 102 | 1f0t | Trypsin | 1 | -8.29 | -6.92 | 2.363 |
| 103 | 1f0u | Trypsin | 1 | -9.89 | -8.98 | 1.599 |
| 104 | 1f3e | t-RNA guanine transglycosylase | 0 | -9.25 | -6.52 | 0.104 |
| 105 | 1fax | Human coagulation factor XA | 0 | -10.07 | -10.6 | 0.521 |
| 106 | 1fkg | FK506 Binding Protein | 0 | -8.81 | -6.57 | 0.256 |
| 107 | 1flr | FAB Fragment | -1 | -6.35 | -6.25 | 0.183 |
| 108 | 1g2k | HIV-1 Protease | 0 | -10.81 | -12.13 | 0.37 |
| 109 | 1ghb | Gamma chymotrypsin | -1 | -1.71 | -6.13 | 0.256 |
| 110 | 1gno | HIV-1 Protease | 1 | -10.57 | -10.1 | 0.29 |
| 111 | 1gpy | Glycogen Phosphorylase | -2 | -6.4 | -7.07 | 0.362 |
| 112 | 1hbv | HIV-1 Protease | 0 | -8.68 | -10.91 | 0.442 |
| 113 | 1hdc | 3 - alpha 20 - beta - hydroxysteroid dehydrogenase | -2 | -8.17 | -8.03 | 0.821 |
| 114 | 1hdt | Alpha Thrombin | 1 | -10.6 | -11.87 | 0.272 |
| 115 | 1hew | Lysozyme | 0 | -8.18 | -8.37 | 0.501 |
| 116 | 1hge | Hemagglutinin | -1 | -3.09 | -4.49 | 0.799 |
| 117 | 1hgh | Hemagglutinin | -1 | -3.89 | -4.7 | 0.204 |
| 118 | 1hgi | Hemagglutinin | -1 | -3.65 | -4.83 | 0.889 |
| 119 | 1hgj | Hemagglutinin | 0 | -2.26 | -3.65 | 0.135 |
| 120 | 1hih | HIV-1 Protease | 0 | -10.97 | -11.8 | 0.204 |
| 121 | 1hii | HIV-2 Protease | 0 | -9.89 | -11.79 | 0.276 |
| 122 | 1hiv | HIV-1 Protease | 0 | -12.64 | -13.14 | 0.344 |
| 123 | 1hos | HIV-1 Protease | -1 | -11.74 | -13.18 | 0.327 |
| 124 | 1hpo | HIV-1 Protease | 0 | -11.82 | -11.14 | 0.388 |
| 125 | 1hps | HIV-1 Protease | 0 | -12.66 | -10.94 | 0.325 |
| 126 | 1hpv | HIV-1 Protease | 0 | -12.58 | -10.83 | 0.189 |
| 127 | 1hpx | HIV-1 Protease | 0 | -12.53 | -13.18 | 0.416 |
| 128 | 1hri | Human Rhinovirus | 1 | -5.91 | -7.67 | 0.208 |
| 129 | 1hrn | Renin | 0 | -10.94 | -11.82 | 0.216 |
| 130 | 1hsg | HIV-1 Protease | 0 | -12.93 | -12.49 | 0.347 |
| 131 | 1hsh | HIV-1 Protease | 1 | -11.69 | -12.07 | 0.332 |
| 132 | 1hte | HIV-1 Protease | 0 | -7.69 | -8.06 | 0.219 |
| 133 | 1htf | HIV-1 Protease | 0 | -11.04 | -9.99 | 0.253 |
| 134 | 1htg | HIV-1 Protease | 0 | -13.21 | -12.86 | 0.44 |
| 135 | 1hvh | HIV-1 Protease | 1 | -10.81 | -12.18 | 0.454 |
| 136 | 1hvi | HIV-1 Protease | 0 | -13.74 | -15.92 | 0.208 |
| 137 | 1hvj | HIV-1 Protease | 0 | -14.26 | -15.02 | 0.206 |
| 138 | 1hvk | HIV-1 Protease | 0 | -13.8 | -15.48 | 0.523 |
| 139 | 1hvl | HIV-1 Protease | 0 | -12.28 | -14.88 | 0.319 |
| 140 | 1hvr | HIV-1 Protease | 0 | -12.97 | -12.96 | 0.195 |
| 141 | 1hxb | HIV-1 Protease | 1 | -13.48 | -12.76 | 0.287 |
| 142 | 1hxw | HIV-1 Protease | 0 | -14.54 | -14.6 | 0.327 |
| 143 | 1ida | HIV-2 Protease | 0 | -11.86 | -12.55 | 0.327 |
| 144 | 1imb | Inositol monophosphatase | -2 | -5.73 | -3.3 | 2.93 |
| 145 | 1ivb | Neuraminidase | -1 | -4.14 | -5.39 | 1.882 |
| 146 | 1ivf | Neuraminidase | -1 | -6.66 | -7.62 | 0.878 |
| 147 | 1k1l | Trypsin | 1 | -9.56 | -7.41 | 0.374 |
| 148 | 1k1n | Trypsin | 0 | -8.82 | -9.47 | 0.341 |
| 149 | 1lyb | Cathepsin D | -1 | -15.57 | -12.36 | 0.219 |
| 150 | 1mcb | Immunoglobulin | -1 | -6.6 | -8.5 | 0.396 |
| 151 | 1mcf | Immunoglobulin | -1 | -7.02 | -8.54 | 0.472 |
| 152 | 1mch | Immunoglobulin | -1 | -7.02 | -8.81 | 0.284 |
| 153 | 1mcj | Immunoglobulin | 0 | -5.16 | -5.92 | 0.381 |
| 154 | 1mcs | Immunoglobulin | -1 | -6.6 | -8.2 | 0.277 |
| 155 | 1mrk | Alpha trichosanthin | 0 | -6.17 | -5.78 | 0.389 |
| 156 | 1mtw | Trypsin | 1 | -10.07 | -7.84 | 1.011 |
| 157 | 1nis | Enolase | -2 | -4.08 | -6.66 | 0.188 |
| 158 | 1nnb | Neuraminidase | -1 | -5.45 | -7.1 | 0.421 |
| 159 | 1nsc | Neuraminidase | -1 | -4.08 | -7.85 | 0.148 |
| 160 | 1ola | Oligopeptide Binding Protein | 1 | -9.54 | -10.16 | 0.248 |
| 161 | 1pdz | Enolase | -3 | -5.03 | -5.8 | 0.381 |
| 162 | 1pgp | 6-Phosphogluconate Dehydrogenase | -3 | -7.77 | -9.15 | 2.368 |
| 163 | 1phh | p-Hydroxybenzoate Hydroxylase | -1 | -3.98 | -4.61 | 0.588 |
| 164 | 1ppc | Trypsin | 1 | -8.8 | -8.46 | 0.415 |
| 165 | 1pph | Trypsin | 1 | -8.48 | -6.35 | 1.454 |
| 166 | 1ppk | Penicillopepsin | 1 | -10.44 | -8.91 | 0.441 |
| 167 | 1ppm | Penicillopepsin | -1 | -7.95 | -9.74 | 0.375 |
| 168 | 1pso | pepsin | -1 | -14.11 | -12.34 | 0.493 |
| 169 | 1qbr | HIV-1 Protease | 0 | -14.42 | -14.54 | 0.331 |
| 170 | 1qbt | HIV-1 Protease | 0 | -14.49 | -14.61 | 0.447 |
| 171 | 1qbu | HIV-1 Protease | 0 | -13.97 | -12.05 | 0.295 |
| 172 | 1rbp | Retinol Binding Protein | 0 | -9.17 | -7.78 | 0.233 |
| 173 | 1rgk | Ribonuclease T1 | -2 | -5.87 | -6.82 | 0.225 |
| 174 | 1rgl | Ribonuclease T1 | -2 | -6.04 | -5.73 | 2.657 |
| 175 | 1rne | Renin | 0 | -11.94 | -15.1 | 0.45 |
| 176 | 1snc | Staphylococcal nuclease | -4 | -9.25 | -11.89 | 0.228 |
| 177 | 1sre | Streptavidin | -1 | -5.45 | -6.19 | 0.266 |
| 178 | 1tlc | Thymidylate Synthase | -2 | -10.98 | -10.08 | 0.392 |
| 179 | 1tng | Trypsin | 1 | -4 | -3.93 | 0.496 |
| 180 | 1tnh | Trypsin | 1 | -4.59 | -4.49 | 0.379 |
| 181 | 1tni | Trypsin | 1 | -2.32 | -3.74 | 0.534 |
| 182 | 1tnj | Trypsin | 1 | -2.67 | -3.72 | 0.316 |
| 183 | 1tnk | Trypsin | 1 | -2.03 | -3.81 | 0.361 |
| 184 | 1tnl | Trypsin | 1 | -2.56 | -3.56 | 1.411 |
| 185 | 1tph | Triose phosphate Isomerase | -3 | -3.1 | -5.21 | 0.381 |
| 186 | 1tpp | Trypsin | 0 | -7.95 | -6.05 | 0.212 |
| 187 | 1ulb | Purine Nucleoside Phosphorylase | 0 | -2.8 | -2.84 | 0.152 |
| 188 | 1uvs | Alpha Thrombin | 0 | -7.41 | -7.53 | 0.716 |
| 189 | 2abh | Phosphate Binding Protein | -2 | -8.88 | -7.38 | 0.571 |
| 190 | 2acs | Aldose Reductase | -3 | -2.75 | -4.8 | 0.775 |
| 191 | 2ak3 | Adenylate kinase | -2 | -5.25 | -9.83 | 0.435 |
| 192 | 2cgr | IGG 2B Fab Fragment | -1 | -9.93 | -10.56 | 0.175 |
| 193 | 2cmd | Malate Dehydrogenase | -3 | -6.24 | -7.77 | 0.347 |
| 194 | 2er7 | Endothiapepsin | -1 | -12.27 | -13.64 | 1.034 |
| 195 | 2gbp | D - Galactose D . Glucose binding protein | 0 | -10.35 | -4.74 | 0.426 |
| 196 | 2ifb | Intestinal Fatty Acid Binding Protein | -1 | -7.41 | -8.07 | 0.368 |
| 197 | 2mcp | Immunoglobulin | -1 | -7.13 | -6.77 | 0.131 |
| 198 | 2pk4 | Human plasminogen | 0 | -5.88 | -2.99 | 0.331 |
| 199 | 2r04 | Rhinovirus 14 | 0 | -8.48 | -7.52 | 0.29 |
| 200 | 2sim | Sialidase | -1 | -8.75 | -6.8 | 0.479 |
| 201 | 2upj | HIV-1 Protease | 0 | -10.14 | -10.7 | 0.493 |
| 202 | 2wea | Penicillopepsin | -1 | -8.37 | -6.48 | 0.248 |
| 203 | 2web | Penicillopepsin | -1 | -7.03 | -9.28 | 0.371 |
| 204 | 2wec | Penicillopepsin | -1 | -6.8 | -6.75 | 0.468 |
| 205 | 2ypi | Triose Phosphate Isomerase | -3 | -6.58 | -7.19 | 0.385 |
| 206 | 3er3 | Endothiapepsin | 1 | -9.68 | -12.89 | 0.884 |
| 207 | 3er5 | Endothiapepsin | 0 | -12.35 | -14.47 | 0.394 |
| 208 | 3ptb | Trypsin | 1 | -6.46 | -5.36 | 0.979 |
| 209 | 4dfr | Dihydrofolate Reductase | -1 | -13.23 | -11.4 | 0.301 |
| 210 | 4er2 | Endothiapepsin | -1 | -11.03 | -10.3 | 0.348 |
| 211 | 4est | Elastase | 0 | -9.55 | -8.08 | 0.509 |
| 212 | 4hmg | Hemagglutinin | -1 | -3.48 | -3.97 | 0.328 |
| 213 | 4phv | HIV-1 Protease | 0 | -12.47 | -12.29 | 0.381 |
| 214 | 4ts1 | Tyrosyl-T / RNA Synthetase | 0 | -7.64 | -4.81 | 0.199 |
| 215 | 5cna | Agglutinin | 0 | -2.73 | -3.71 | 0.77 |
| 216 | 5enl | Enolase | -3 | -5.24 | -6.59 | 1.05 |
| 217 | 5hvp | HIV-1 Protease | -1 | -10.51 | -12.9 | 0.22 |
| 218 | 5tim | Triose Phosphate Isomerase | -2 | -3.14 | -3.09 | 0.543 |
| 219 | 6enl | Enolase | -3 | -4.14 | -5.53 | 0.506 |
| 220 | 6rnt | Ribonuclease | -2 | -8.67 | -7.26 | 0.315 |
| 221 | 6tim | Triose phosphate isomerase | -2 | -4.37 | -7.59 | 0.323 |
| 222 | 7dfr | Dihydrofolate Reductase | -2 | -10.09 | -10.73 | 0.292 |
| 223 | 7gpb | Glycogen Phosphorylase | -2 | -7.53 | -7.64 | 0.943 |
| 224 | 7tim | Triose phosphate isomerase | -2 | -7.35 | -7.01 | 0.12 |
| 225 | 8gpb | Glycogen Phosphorylase | -2 | -4.91 | -5.96 | 0.53 |
| 226 | 9hvp | HIV-1 Protease | 0 | -11.38 | -13.9 | 0.515 |