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

BMC Bioinformatics

Table 13 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 extended 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	21	0.635	0.538	0.585	0.520	-0.050	-0.018	0.528	0.567	0.465	0.462	0.684	0.620	0.636	0.695	0.316	0.380	0.364	0.305
FN096	24	0.632	0.526	0.585	0.516	-0.046	-0.010	0.468	0.343	0.472	0.484	0.678	0.605	0.450	0.406	0.322	0.395	0.550	0.594
FN339	24	0.606	0.501	0.585	0.516	-0.021	-0.015	0.426	0.302	0.472	0.484	0.614	0.439	0.386	0.332	0.386	0.561	0.614	0.668

ISSN: 1471-2105