Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

Table 2 Accuracy of virtual screening by Vina for the DUD-E dataset. Experimental and predicted binding sites are used in molecular docking with the default and optimized box sizes. Average values and the corresponding standard deviations are reported; p-values are calculated using the Wilcoxon signed-rank test

Metric	Dataset^a	Experimental binding sites			Predicted binding sites
Metric	Dataset^a	Default	Optimized	p-value	Default	Optimized	p-value
EF^1 %	D77	8.126 ± 7.881	8.131 ± 7.567	0.795	7.670 ± 7.886	8.205 ± 8.245	0.108
EF^1 %	D101	7.714 ± 8.311	7.782 ± 7.806	1.000	-	-	-
EF^10 %	D77	3.324 ± 1.738	3.443 ± 1.827	0.142	3.193 ± 1.701	3.283 ± 1.754	0.073
EF^10 %	D101	3.137 ± 1.717	3.295 ± 1.815	0.034	-	-	-
BEDROC20	D77	0.229 ± 0.140	0.234 ± 0.141	0.274	0.218 ± 0.136	0.229 ± 0.142	0.041
BEDROC20	D101	0.214 ± 0.138	0.223 ± 0.140	0.067	-	-	-
AUC	D77	0.697 ± 0.130	0.703 ± 0.123	0.065	0.688 ± 0.130	0.689 ± 0.131	0.082
AUC	D101	0.690 ± 0.125	0.697 ± 0.118	0.006	-	-	-
ACT-50 %	D77	0.244 ± 0.165	0.234 ± 0.151	0.030	0.251 ± 0.160	0.251 ± 0.163	0.101
ACT-50 %	D101	0.254 ± 0.159	0.240 ± 0.146	0.006	-	-	-

^aD77 is the subset of DUD-E containing only those proteins whose binding sites are detected by eFindSite, D101 is the entire DUD-E dataset

ISSN: 1758-2946