Table 2 The performance of best docking pose generated by different docking methods using blind docking on the PPDbench dataset
From: Benchmarking of different molecular docking methods for protein-peptide docking
Docking methods | FNAT | L-RMSD | I-RMSD | % Success |
|---|---|---|---|---|
ATTRACT-20a | 66.51 | 6.16 | 6.12 | 54.13 |
ATTRACT-10 | 57.44 | 8.86 | 8.75 | 48.87 |
ATTRACT-5 | 53.01 | 10.38 | 10.23 | 42.10 |
ATTRACT-3 | 48.95 | 11.74 | 11.53 | 39.09 |
ATTRACT-1 | 40.86 | 15.59 | 15.30 | 34.58 |
Hex-20 | 30.92 | 25.73 | 25.64 | 18.04 |
Hex-10 | 26.62 | 27.85 | 27.82 | 17.29 |
Hex-5 | 21.33 | 30.37 | 30.31 | 15.03 |
Hex-3 | 17.88 | 31.77 | 31.70 | 12.78 |
Hex-1 | 13.06 | 35.64 | 35.55 | 10.52 |
ZDOCK-20 | 69.67 | 7.53 | 7.40 | 63.90 |
ZDOCK-10 | 61.79 | 9.42 | 9.27 | 53.38 |
ZDOCK-5 | 57.16 | 10.87 | 10.78 | 48.87 |
ZDOCK-3 | 54.14 | 11.97 | 11.84 | 42.85 |
ZDOCK-1 | 42.88 | 15.85 | 15.74 | 32.33 |
PatchDock-20 | 55.99 | 7.98 | 7.79 | 26.31 |
PatchDock-10 | 48.01 | 9.93 | 9.78 | 21.05 |
PatchDock-5 | 39.78 | 12.45 | 12.30 | 18.79 |
PatchDock-3 | 34.55 | 14.61 | 14.39 | 17.29 |
PatchDock-1 | 21.83 | 19.97 | 19.71 | 11.27 |
pepATTRACT-20 | 27.25 | 13.76 | 13.57 | 1.50 |
pepATTRACT-10 | 22.70 | 16.04 | 15.84 | 1.50 |
pepATTRACT-5 | 18.67 | 18.24 | 18.07 | 1.50 |
pepATTRACT-3 | 16.22 | 19.55 | 19.31 | 0.75 |
pepATTRACT-1 | 12.32 | 22.12 | 21.88 | 0.00 |
FRODOCK-20 | 71.44 | 3.72 | 3.69 | 55.63 |
FRODOCK-10 | 70.79 | 4.06 | 3.94 | 55.63 |
FRODOCK-5 | 64.16 | 6.04 | 5.92 | 50.37 |
FRODOCK-3 | 62.92 | 6.79 | 6.69 | 50.37 |
FRODOCK-1 | 48.40 | 12.46 | 12.21 | 39.09 |