Table 1. Comparison of Galaxy7TM with AutoDock Vina applied to input GPCR structures (Input-Vina) and to GPCR structures refined by MPrelax (MPrelax-Vina), respectively, in terms of docking accuracy and comparison with GalaxyRefine and MPrelax in terms of improvement in receptor structure quality for full structure (and for binding pocket residues in parentheses) on a test set of 125 GPCR structure-ligand inputs.
| Percentage of successful cases for the best of 10 predictions | |||
|---|---|---|---|
| Docking accuracy | Galaxy7TM | Input-Vina | MPrelax-Vina |
| Ligand RMSD (≤2.0Å) | 20.8 | 16.0 | 6.4 |
| Contact ratio (≥30.0%) | 24.8 | 15.2 | 12.0 |
| Improvement in receptor structure quality | Galaxy7TM | GalaxyRefine | MPrelax |
| ΔGDT-HA (>0.0) | 78.4 (68.0) | 77.6 (55.2) | 46.4 (52.8) |
| ΔGDC-SC (>0.0) | 93.6 (88.8) | 84.0 (52.8) | 84.8 (80.0) |
| ΔCα-RMSD (<0.0) | 74.4 (75.2) | 71.2 (64.8) | 62.4 (60.8) |