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

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

Receptor structure	Input ligand structure	Method	RMSD (Å)		Center distance (Å)		Average RMSD < 2.0 (or 5.0 Å)
Receptor structure	Input ligand structure	Method	Ave	Med	Ave	Med	Average RMSD < 2.0 (or 5.0 Å)
Holo-protein structure (315)	Crystal	EDock	4.75	4.29	2.44	1.59	96
Holo-protein structure (315)	Crystal	Vina	4.79	4.69	2.14	1.55	74
Holo-protein structure (315)	Random	EDock	4.81	4.59	2.51	1.83	74
Holo-protein structure (315)	Random	Vina	4.84	4.81	2.17	1.55	63
Predicted structure (180)	Crystal	EDock	4.85	4.42	2.72	2.11	101
Predicted structure (180)	Crystal	Vina	6.24	6.37	3.48	3.19	56
Predicted structure (180)	Random	EDock	5.09	4.99	2.77	2.27	90
Predicted structure (180)	Random	Vina	6.47	6.45	3.52	3.07	40

“Crystal” and “Random” represent the real ligand conformation and random rotatable conformation, respectively. The best performance is highlighted in italic font in each category

ISSN: 1758-2946