Table 6.
Ligand RMSD (Å) Values of Top 10 Poses after Pose Clustering, MD Simulation, and Post-MD Rescoring for 1S3K and 3TV3a
| 1S3K | 3TV3 | ||||
|---|---|---|---|---|---|
| RMSD before MD (sorted by rank) | RMSD after MD (rescored rank) | RMSD after MD (sorted by rank) | Before MD (sorted by rank) | RMSD after MD (rescored rank) | After MD (sorted by rank) |
| 6.2 (1) | 5.9 (4) | 1.1 (1) | 17.4 (1) | 18.2 (S) | 0.8 (1) |
| 0.7 (2) | 1.1 (1) | 6.7 (2) | 6.5 (2) | 6.0 (7) | 23.4 (2) |
| 5.4 (3) | 7.0 (S) | 7.5 (3) | 1.4 (3) | 0.8 (1) | 23.0 (3) |
| 6.4 (4) | 6.7 (2) | 5.9 (4) | 22.8 (4) | 23.4 (2) | 17.7 (4) |
| 5.6 (5) | 7.6 (6) | 7.0 (5) | 22.2 (5) | 23.0 (3) | 18.2 (5) |
| 6.9 (6) | 8.0 (9) | 7.6 (6) | 17.3 (6) | 17.7 (4) | 18.3 (6) |
| 7.0 (7) | 7.5 (3) | 4.9 (7) | 22.1 (7) | 24.1 (8) | 6.0 (7) |
| 4.2 (8) | 4.9 (7) | 7.6 (8) | 24.3 (8) | 18.3 (6) | 24.1 (8) |
| 6.3 (9) | 7.6 (8) | 8.0 (9) | 23.6 (9) | 24.9 (9) | 24.9 (9) |
| 5.0 (10) | 9.1 (10) | 9.1 (10) | 6.7 (10) | 43.0 (10) | 43.0 (10) |
a
Acceptable poses and poses that worsened by 2 Å from their initial position during MD are bolded.