Grading amino acid properties increased accuracies of single point mutation on protein stability prediction

BMC Bioinformatics

Table 1 Cross-validation performance of the sequence-based SVM method of different encoding schemes

Encoding scheme	Q₃	MCC	Q(N)	Q(+)	Q(-)	Specificity (N)	Specificity (+)	Specificity (-)	PPV (P (N))	PPV (P (+))	PPV (P (-))	NPV (N)	NPV (+)	NPV (-)	MCC (C(N))	MCC (C(+))	MCC (C(-))
Capriotti^¶	56.00	0.27	48.00	54.00	54.00	62.00	44.00	44.00	-	-	-	-	-	-	0.17	0.29	0.29
Sparse	56.81	0.28	58.85	54.12	53.51	61.34	79.31	81.10	65.35	65.11	62.31	62.40	75.16	72.37	0.21	0.31	0.33
11-factors	56.92	0.28	59.07	52.32	51.27	63.56	80.77	82.87	68.29	65.46	60.17	63.32	72.32	71.37	0.19	0.32	0.33
HEC	56.91	0.29	58.32	50.56	52.47	66.55	81.39	80.34	65.28	65.43	63.45	65.79	74.56	71.57	0.21	0.32	0.32
K-D	55.98	0.25	57.81	51.64	49.73	63.72	78.29	81.57	63.54	62.14	63.30	66.57	73.22	71.11	0.20	0.34	0.31
AAproperty15	59.57	0.31	61.72	56.13	57.40	60.96	79.57	81.48	68.16	65.89	67.87	65.02	76.83	76.71	0.30	0.35	0.34
AAproperty15Grade	63.63	0.36	64.15	58.23	57.62	61.95	80.35	82.07	69.81	62.52	69.12	67.18	78.31	78.96	0.34	0.39	0.36

All numbers except MCC represent per cent values. +, - and N: the indexes are evaluated for increasing, decreasing or neutral protein free energy stability change, respectively according to the classification described in section 2 of Results and Discussions; for the definition of the different indexes see the Scoring the performance in Methods. ^¶ data from Capriotti [19]

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