Table 3.
The performance best docking pose generated by different docking methods using re-docking on the PPDbench dataset
| Docking methods | FNAT | L-RMSD | I-RMSD | % Success |
|---|---|---|---|---|
| Hex-20a | 78.66 | 4.55 | 4.44 | 69.17 |
| Hex-10 | 75.73 | 5.25 | 5.18 | 66.17 |
| Hex-5 | 71.24 | 6.50 | 6.41 | 65.41 |
| Hex-3 | 66.76 | 7.74 | 7.66 | 61.65 |
| Hex-1 | 59.44 | 10.63 | 10.49 | 56.39 |
| ZDOCK-20 | 89.61 | 2.88 | 2.81 | 85.71 |
| ZDOCK-10 | 84.55 | 3.85 | 3.76 | 78.95 |
| ZDOCK-5 | 80.77 | 5.14 | 5.04 | 75.19 |
| ZDOCK-3 | 79.06 | 5.67 | 5.56 | 69.92 |
| ZDOCK-1 | 68.44 | 8.60 | 8.44 | 55.64 |
| PatchDock-20 | 63.14 | 5.14 | 5.05 | 32.33 |
| PatchDock-10 | 55.64 | 6.73 | 6.63 | 29.32 |
| PatchDock-5 | 48.30 | 8.22 | 8.08 | 24.81 |
| PatchDock-3 | 43.25 | 9.46 | 9.27 | 23.31 |
| PatchDock-1 | 29.03 | 13.36 | 13.13 | 18.80 |
| pepATTRACT-20 | 39.07 | 8.21 | 8.07 | 3.76 |
| pepATTRACT-10 | 34.82 | 9.17 | 9.02 | 2.26 |
| pepATTRACT-5 | 30.32 | 10.03 | 9.83 | 2.26 |
| pepATTRACT-3 | 27.20 | 10.87 | 10.70 | 2.26 |
| pepATTRACT-1 | 21.11 | 12.32 | 12.07 | 1.50 |
aNumber indicate number of top docking poses generated by method