Table 4:
Summary of docking results for the flexible and rigid-body docking at the “short”, “medium” and “long” levels using Autodock regarding the AUC, EF and EF’ values with 5% and 10% of sampled compounds calculated using different GaMD simulation ensembles of the A1AR. Among the listed 30 docking performance metrics, 26 of them (highlighted in bold) showed better performance using flexible docking than using rigid docking, while only 3 and 1 of them showed the same and decreased performance values, respectively.
| System | Levels of Docking | ADO-A1AR-Gi (NAMD, GaMD_Dih) | ADO-A1AR-Gi (NAMD, GaMD_Dual) | ADO-A1AR-Gi (AMBER, GaMD_Dih) | ADO-A1AR-Gi (AMBER, GaMD_Dual) | ADO-A1AR-Gi-VCP171 (AMBER, GaMD_Dih) | ADO-A1AR-Gi-VCP171 (AMBER, GaMD_Dual) |
|---|---|---|---|---|---|---|---|
| AUC | Short | 0.45 | 0.45 | 0.46 | 0.43 | 0.47 | 0.44 |
| Medium | 0.49 | 0.49 | 0.50 | 0.50 | 0.50 | 0.48 | |
| Long | 0.50 | 0.50 | 0.50 | 0.54 | 0.50 | 0.52 | |
| Flexible | 0.53 | 0.53 | 0.52 | 0.51 | 0.54 | 0.60 | |
| EF (5%) | Short | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| Medium | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | |
| Long | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | |
| Flexible | 0.80 | 0.80 | 0.00 | 0.80 | 0.80 | 0.80 | |
| EF’ (5%) | Short | 0.78 | 0.78 | 0.39 | 0.47 | 0.42 | 0.37 |
| Medium | 0.95 | 0.95 | 0.54 | 0.89 | 1.11 | 1.14 | |
| Long | 0.10 | 0.10 | 0.59 | 1.36 | 0.87 | 0.88 | |
| Flexible | 5.00 | 5.00 | 1.47 | 6.58 | 3.97 | 8.33 | |
| EF (10%) | Short | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| Medium | 0.00 | 0.00 | 0.00 | 0.00 | 0.40 | 0.40 | |
| Long | 0.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | |
| Flexible | 0.40 | 0.40 | 0.40 | 0.40 | 0.40 | 0.80 | |
| EF’ (10%) | Short | 0.96 | 0.96 | 0.75 | 0.71 | 0.77 | 0.66 |
| Medium | 1.12 | 1.12 | 0.93 | 1.06 | 1.16 | 1.13 | |
| Long | 0.20 | 0.20 | 0.96 | 1.69 | 1.11 | 1.03 | |
| Flexible | 3.05 | 3.05 | 1.98 | 2.46 | 2.32 | 4.98 |