Table 5.
Autodock 3 performance with de novo solvent placement
| PDB ID | W− top posea RMSD (Å) | W+ top poseb RMSD (Å) | W− best pose ranka (RMSD (Å)) | W+ best pose rankb (RMSD (Å)) | W− correct posesa in top 50 | W+ correct posesb in top 50 | W− correct posesa in top 10 | W+ correct posesb in top 10 |
|---|---|---|---|---|---|---|---|---|
| 1DBO | 1.93 | 1.42 | 42 (1.27) | 11 (1.06) | 15 | 27 | 0 | 6 |
| 1OJN | 2.90 | 1.37 | 8 (1.11) | 2 (1.13) | 6 | 9 | 4 | 6 |
| 1RWH | 1.99 | 1.13 | 7 (0.97) | 2 (0.87) | 8 | 13 | 7 | 9 |
| 1G5N | 4.41 | 4.28 | 29 (1.48) | 27 (1.82) | 5 | 5 | 1 | 1 |
| 1T8U | 2.10 | 3.57 | 2 (1.84) | 3 (2.27) | 4 | 2 | 3 | 1 |
| 3E7J | 1.79 | 1.20 | 1 (1.79) | 1 (1.20) | 5 | 3 | 2 | 3 |
| 2HYU | 2.26 | 3.60 | 16 (1.91) | 4 (2.29) | 8 | 7 | 2 | 3 |
| 2BRS | 2.77 | 3.01 | 34 (1.13) | 15 (1.45) | 8 | 16 | 0 | 8 |
| 1BFB | 3.35 | 3.58 | 14 (1.88) | 6 (2.31) | 5 | 3 | 4 | 1 |
| 3IN9_1 | 3.54 | 2.75 | 32 (0.87) | 34 (0.87) | 20 | 16 | 0 | 2 |
| 3IN9_2 | 1.18 | 1.22 | 22 (0.99) | 13 (0.85) | 32 | 43 | 9 | 10 |
| Mean | 2.57 ± 0.93 | 2.47 ± 1.21 | 19 (1.39 ± 0.41) | 11 (1.47 ± 0.60) | 10.5 | 13.1 | 2.9 | 4.5 |
aDocking runs without explicit solvent
bDocking runs with explicit solvent