Computational and Mathematical Methods in Medicine

Research Article

NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches

Table 2

Comparison of the predictive qualities of the NSiteMatch, MetaPocket, Findsite, and Q-SiteFinder for the prediction of binding residues for ADP, ATP, and AMP. The PRE, REC, and MCC stand for precision, recall, and Matthews Correlation Coefficient, respectively. The NSiteMatch generates a real value for each residue (propensity to bind), which is thresholded to make binary (binding versus nonbinding residue) predictions. The rows annotated as the “NSiteMatch^p” are based on the thresholds that generate precision values which match the highest precision obtained by the MetaPocket, Findsite, and Q-SiteFinder for a given ligand type; similarly, the “NSiteMatch^r” rows correspond to thresholds for which the highest value of recall is matched. The matching recall and precision values are shown in italics and the highest MCC values are given in bold font.


Ligand	Method	40%			Family			Superfamily			Fold
type	Method	PRE	REC	MCC	PRE	REC	MCC	PRE	REC	MCC	PRE	REC	MCC

ADP	NSiteMatch^p	0.48	0.79	0.6	0.43	0.68	0.52	0.43	0.49	0.44	0.43	0.48	0.43
	NSiteMatch^r	0.76	0.53	0.62	0.53	0.57	0.53	0.37	0.57	0.43	0.37	0.57	0.43
	MetaPocket	0.41	0.13	0.21	0.43	0.13	0.22	0.43	0.13	0.22	0.43	0.13	0.22
	Findsite	0.48	0.67	0.55	0.41	0.45	0.42	0.31	0.32	0.3	0.31	0.3	0.3
	Q-SiteFinder	0.29	0.53	0.36	0.31	0.57	0.39	0.31	0.57	0.39	0.31	0.57	0.39

ATP	NSiteMatch^p	0.49	0.68	0.56	0.46	0.54	0.47	0.46	0.41	0.41	0.46	0.41	0.41
	NSiteMatch^r	0.61	0.52	0.54	0.47	0.51	0.47	0.4	0.51	0.42	0.4	0.51	0.42
	MetaPocket	0.47	0.16	0.26	0.46	0.14	0.23	0.46	0.14	0.23	0.46	0.14	0.23
	Findsite	0.49	0.52	0.5	0.38	0.43	0.39	0.29	0.34	0.31	0.29	0.34	0.31
	Q-SiteFinder	0.31	0.52	0.36	0.29	0.51	0.35	0.29	0.51	0.35	0.29	0.51	0.35

AMP	NSiteMatch^p	0.47	0.62	0.51	0.47	0.36	0.39	0.47	0.3	0.35	0.47	0.28	0.34
	NSiteMatch^r	0.47	0.62	0.51	0.33	0.6	0.41	0.29	0.6	0.38	0.29	0.6	0.38
	MetaPocket	0.47	0.16	0.26	0.47	0.15	0.25	0.47	0.15	0.25	0.47	0.15	0.25
	Findsite	0.44	0.49	0.44	0.31	0.34	0.31	0.29	0.33	0.3	0.29	0.32	0.29
	Q-SiteFinder	0.29	0.62	0.39	0.29	0.6	0.38	0.29	0.6	0.38	0.29	0.6	0.38