Table 1.
Comparison of the efficacy of the programs
| Programs: sampling methods and scoring functions | Conformational sampling | Scoring | |||
|---|---|---|---|---|---|
| 1-Number of poses obtained | 2-Number of correct poses | 3-Number of targets with a correct pose | 4-Number of targets with a correct pose ranked in the top 4 | 5-Number of targets with a correct pose ranked as the top 1 | |
| FlexX | 2915 | 910 | 65 | ||
| FlexX | 57 | 52 | |||
| Surflex | 2899 | 1152 | 84 | ||
| Surflex | 72 | 56 | |||
| Glide-SP | 2393 | 624 | 79 | ||
| Glidescore | 75 | 65 | |||
| Emodel | 72 | 65 | |||
| Glide-XP | 392 | 210 | 74 | ||
| Glidescore | 73 | 68 | |||
| Emodel | 73 | 66 | |||
| Gold | 1447 | 330 | 77 | ||
| PLP | 74 | 64 | |||
| Goldscore | 73 | 60 | |||
| USC based on docking results | 87 | ||||
The comparison is made for ligand conformational sampling (columns 1–3) and pose scoring (columns 4 and 5). From the requested 3000 poses per program (30 poses per target, for 100 targets), the number of obtained poses is given in the first column. Of these poses a certain number is correct, with RMSD < 2 Å from the crystal position, (column 2) and corresponding to a number of targets (column 3). The number of targets whose correct poses are ranked in the top 4 are given in column 4 and those whose correct poses are top-ranked are given in column 5. The number of targets with a correct pose obtained with the USC method, based on the docking results, is reported in the last line (see the “USC method” section below)