Table 2.
Docking unbound subunits
| Receptor | Ligand | ICM dockinga | Other docking methodsb | ||||||||
| Complex PDB | PDB | Res (Å) | PDB | Res (Å) | Original maps | Optimized maps | Refinement | Nussinovc | FTDOCKd | FTDOCKe | BiGGERf |
| Protease-inhibitor | |||||||||||
| 1ca0 | 5cha | 1.67 | 1aap | 1.50 | 24 of 4153 (1.7) | 6 of 228 (1.4) | 1 of 228 (1.2) | — | — | — | — |
| 1cbw | 5cha | 1.67 | 1bpi | 1.10 | 167 of 5492 (1.2) | 5 of 231 (0.9) | 1 of 231 (0.7) | — | — | — | — |
| 1acb | 5cha | 1.67 | 1egl | NMR | 3981 of 4511 (B.D.)g | 135 of 239 (B.D.)g | 102 of 239 (Backbone Def.)g | — | — | — | — |
| 1cho | 5cha | 1.67 | 1omu | NMR | 10 of 5063 (1.2) | 7 of 242 (2.6) | 1 of 242 (1.0) | 2 of 2289 (1.6) | 11 of 86 (1.2) | 1 of 86 (1.3) | 6 of 1000 (2.9) |
| 1cgi | 1chg | 2.50 | 1hpt | 2.30 | 18 of 5261 (3.6) | 8 of 256 (3.4) | 12 of 256 (3.1) | — | 3 of 94 (1.8) | 3 of 94 (2.2) | 9 of 1000 (3.7) |
| 2kai | 2pka | 2.05 | 1bpi | 1.10 | 823 of 4078 (3.8) | 36 of 241 (4.1) | 2 of 241 (5.5) | 9 of 4222 (1.2) | 130 of 364 (1.5) | 2 of 364 (1.3) | Not found |
| 2sni | 2st1 | 1.80 | 2ci2 | 2.00 | 243 of 4286 (2.9) | 66 of 220 (2.5) | 1 of 220 (2.9) | 92 of 3582 (2.6) | 8 of 26 (1.8) | 4 of 26 (2.6) | 16 of 1000 (1.3) |
| 2sic | 2st1 | 1.80 | 3ssi | 2.30 | 67 of 4109 (2.4) | 37 of 223 (2.4) | 7 of 223 (1.9) | — | Not found | — | 15 of 1000 (3.3) |
| 1cse | 1sbc | 2.50 | 1egl | NMR | 70 of 7378 (B.D.)g | 167 of 246 (B.D.)g | 40 of 246 (Backbone Def.)g | — | — | — | — |
| 2tec | 1thm | 1.37 | 1egl | NMR | 172 of 5613 (B.D.)g | 175 of 247 (B.D.)g | 146 of 247 (Backbone Def.)g | — | — | — | — |
| 1taw | 5ptp | 1.34 | 1aap | 1.50 | 288 of 4086 (2.2) | 1 of 228 (3.5) | 1 of 228 (2.9) | — | — | — | — |
| 2ptc | 5ptp | 1.34 | 1bpi | 1.10 | 569 of 4632 (1.8) | 41 of 229 (1.0) | 3 of 229 (2.0) | 1 of 3453 (1.2) | 16 of 229 (1.5) | 11 of 229 (1.6) | 52 of 1000 (2.7) |
| 3tgi | 1ane | 2.20 | 1bpi | 1.10 | 1756 of 5718 (1.1) | 23 of 243 (0.6) | 1 of 243 (0.8) | — | — | — | — |
| 1brc | 1bra | 2.20 | 1aap | 1.50 | 87 of 4651 (2.3) | 1 of 237 (3.7) | 1 of 237 (1.8) | — | — | — | — |
| Enzyme-inhibitor | |||||||||||
| 1fss | 2ace | 2.50 | 1fsc | 2.00 | 66 of 6649 (1.7) | 51 of 264 (1.5) | 7 of 264 (1.7) | — | — | — | 11 of 1000 (3.2) |
| 1bvn | 1pif | 2.30 | 2ait | NMR | 2689 of 5858 (1.8) | 2 of 265 (5.0) | 7 of 265 (5.0) | — | — | — | — |
| 1bgs | 1a2p | 1.50 | 1a19 | 2.76 | 139 of 6279 (3.9) | 55 of 290 (3.4) | 212 of 290 (4.2) | — | — | — | 35 of 1000 (1.9) |
| 1ay7 | 1rge | 1.15 | 1a19 | 2.76 | 484 of 4765 (3.9) | 208 of 284 (5.2) | 156 of 284 (6.2) | — | — | — | — |
| TEM1h | retmh | 1.90 | bliph | 2.10 | 1 of 4512 (2.4) | 2 of 240 (2.8) | 12 of 240 (3.1) | — | — | — | — |
| 1ugh | 1akz | 1.57 | 2ugi | 2.20 | 72 of 6560 (2.4) | 9 of 300 (2.8) | 9 of 300 (4.8) | — | — | — | — |
| Electron transport | |||||||||||
| 2pcb | 1ccp | 2.20 | 1hrc | 1.90 | 3307 of 5193 (2.3) | 80 of 252 (4.1) | 46 of 252 (3.2) | — | — | — | 18 of 1000 (2.4) |
| 2pcf | 1ctm | 2.30 | 1ag6 | 1.70 | 19 of 6037 (5.3) | 58 of 283 (4.9) | 9 of 283 (5.2) | — | — | — | — |
| Antibody-antigen | |||||||||||
| 1mlc | 1mlb | 2.10 | 1lza | 1.60 | 2435 of 5099 (3.3) | 21 of 259 (5.3) | 16 of 259 (5.1) | — | 41 of 590 (1.2) | — | Not found |
| 1vfb | 1vfa | 1.80 | 11za | 1.60 | 51 of 4253 (B.D.)g | 30 of 291 (B.D.)g | 75 of 291 (Backbone Def.)g | — | 176 of 707 (2.1) | — | Not found |
a Rank of best solution and total number of conformations obtained in this work; in parentheses: r.m.s.d. (Å) calculated for the ligand interface Cα atoms of the best solution when only the receptor Cα atoms are superimposed onto the equivalent atoms of the real structure.
b This is not a comparison between different docking methods, but rather a compilation of the results. The receptor coverage/restraints differ between the algorithms, so a direct comparison between the results could be misleading.
c Global docking followed by hydrophobicity and connectivity filters (Norel et al. 1999); r.m.s.d. (Å) calculated for ligand heavy atoms when only receptor is superimposed onto the real structure.
d Global docking and filtering with distance restraints (Gabb et al. 1997); r.m.s.d. (Å) calculated for all Cα atoms when both receptor and ligand Cα atoms are superimposed onto the real complex.
e Global docking, filtering with distance restraints and refinement with solvation (Jackson et al. 1998); r.m.s.d. (Å) calculated for all Cα atoms when both receptor and ligand Cα atoms are superimposed onto the real complex.
f Global docking (Palma et al. 2000); r.m.s.d. (Å) calculated for the ligand Cα atoms when only the receptor Cα atoms are superimposed onto the real structure.
g Ligand backbone deformation upon binding (r.m.s.d. of the unbound ligand backbone atoms in the interface >1.8 Å from the complexed ligand structure).
h No coordinates deposited in PDB: the structures were kindly provided by the authors (Strynadka et al. 1992, 1994, 1996b).