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Table 4 Summary of flexible docking results of EDock compared with Vina

From: EDock: blind protein–ligand docking by replica-exchange monte carlo simulation

Receptor structureInput ligand structureMethodRMSD (Å)Center distance (Å)Average RMSD < 2.0 (or 5.0 Å)
AveMedAveMed
Holo-protein structure (315)CrystalEDock4.754.292.441.5996
Vina4.794.692.141.5574
Holo-protein structure (315)RandomEDock4.814.592.511.8374
Vina4.844.812.171.5563
Predicted structure (180)CrystalEDock4.854.422.722.11101
Vina6.246.373.483.1956
Predicted structure (180)RandomEDock5.094.992.772.2790
Vina6.476.453.523.0740
  1. “Crystal” and “Random” represent the real ligand conformation and random rotatable conformation, respectively. The best performance is highlighted in italic font in each category