Table 5 The performance of best docking pose generated by different methods and difference in performance of docking poses generated in two events on the PPDbench dataset
From: Benchmarking of different molecular docking methods for protein-peptide docking
Docking Method | First Docking | Second Docking | Difference (First-Second) | ||||||
|---|---|---|---|---|---|---|---|---|---|
FNAT | L-RMSD | I-RMSD | FNAT | L-RMSD | I-RMSD | FNAT | L-RMSD | I-RMSD | |
ATTRACT-20a | 66.51 | 6.16 | 6.12 | 66.51 | 6.16 | 6.12 | 0.00 | 0.00 | 0.00 |
ATTRACT-1 | 40.86 | 15.59 | 15.30 | 40.86 | 15.59 | 15.30 | 0.00 | 0.00 | 0.00 |
Hex-20 | 30.92 | 25.73 | 25.64 | 30.60 | 25.77 | 25.72 | 0.32 | 0.04 | 0.08 |
Hex-1 | 13.06 | 35.64 | 35.55 | 12.33 | 35.39 | 35.38 | 0.73 | 0.25 | 0.17 |
ZDOCK-20 | 69.67 | 7.53 | 7.40 | 69.68 | 7.53 | 7.40 | 0.01 | 0.00 | 0.00 |
ZDOCK-1 | 42.88 | 15.85 | 15.74 | 42.86 | 15.85 | 15.74 | 0.02 | 0.00 | 0.00 |
PatchDock-20 | 55.99 | 7.98 | 7.79 | 56.00 | 7.98 | 7.79 | 0.01 | 0.00 | 0.00 |
PatchDock-1 | 21.83 | 19.97 | 19.71 | 21.87 | 19.97 | 19.71 | 0.04 | 0.00 | 0.00 |
pepATTRACT-20 | 27.25 | 13.76 | 13.57 | 27.26 | 13.76 | 13.57 | 0.01 | 0.00 | 0.00 |
pepATTRACT-1 | 12.32 | 22.12 | 21.88 | 12.33 | 22.12 | 21.88 | 0.01 | 0.00 | 0.00 |
FRODOCK-20 | 71.44 | 3.72 | 3.69 | 71.44 | 3.72 | 3.69 | 0.00 | 0.03 | 0.00 |
FRODOCK-1 | 48.40 | 12.46 | 12.21 | 48.39 | 12.46 | 12.21 | 0.01 | 0.00 | 0.00 |