FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

BMC Bioinformatics

Table 12 What is the effect on FunFOLD performance if the native structures are used for each target? A repeat comparison of FunFOLD performance versus the top 3 groups for at CASP9 using partial binding site definitions.

Group ID	N	Mean score for group		Mean score for FunFOLD		Difference in mean score		Mean Z-score for group		Mean Z-score for FunFOLD		P-value (raw score)		P-value (Z-score)		1 - p-value (raw score)		1 - p-value (Z-score)
		MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT
FN035	22	0.714	0.644	0.621	0.541	-0.092	-0.103	0.627	0.627	0.387	0.197	0.649	0.869	0.784	0.889	0.351	0.131	0.216	0.111
FN096	25	0.696	0.620	0.617	0.534	-0.079	-0.086	0.555	0.499	0.404	0.250	0.674	0.850	0.594	0.771	0.326	0.150	0.406	0.229
FN339	25	0.668	0.606	0.617	0.534	-0.051	-0.072	0.462	0.482	0.404	0.250	0.614	0.837	0.500	0.771	0.386	0.163	0.500	0.229

ISSN: 1471-2105