MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs

BMC Systems Biology

Table 3 Five-fold cross-validation results of the SVM models trained with various features for discriminating between positive and negative training datasets

Residue	Training features	Sn	Sp	Acc	MCC	AUC
K	Amino acid composition (AAC)	0.70	0.69	0.69	0.37	0.78
	Amino acid pairs composition (AAPC)	0.66	0.65	0.65	0.29	0.71
	Amino acid sequence (AA)	0.68	0.64	0.65	0.23	0.67
	Positional weighted matrix (PWM)	0.74	0.67	0.69	0.37	0.78
	Position specific scoring matrix (PSSM)	0.63	0.61	0.62	0.16	0.61
	BLOSUM62 (B62)	0.63	0.60	0.61	0.15	0.59
R	Amino acid composition (AAC)	0.66	0.63	0.64	0.28	0.70
	Amino acid pairs composition (AAPC)	0.62	0.61	0.61	0.22	0.65
	Amino acid sequence (AA)	0.62	0.62	0.62	0.17	0.62
	Positional weighted matrix (PWM)	0.71	0.70	0.70	0.39	0.80
	Position specific scoring matrix (PSSM)	0.61	0.56	0.58	0.14	0.59
	BLOSUM62 (B62)	0.62	0.62	0.62	0.17	0.62
T	Amino acid composition (AAC)	0.74	0.70	0.72	0.41	0.82
	Amino acid pairs composition (AAPC)	0.69	0.68	0.69	0.35	0.75
	Amino acid sequence (AA)	0.63	0.62	0.62	0.18	0.63
	Positional weighted matrix (PWM)	0.69	0.67	0.68	0.32	0.73
	Position specific scoring matrix (PSSM)	0.65	0.65	0.65	0.29	0.70
	BLOSUM62 (B62)	0.58	0.50	0.53	0.08	0.53
P	Amino acid composition (AAC)	0.72	0.70	0.70	0.39	0.80
	Amino acid pairs composition (AAPC)	0.68	0.64	0.65	0.30	0.71
	Amino acid sequence (AA)	0.64	0.66	0.65	0.23	0.67
	Positional weighted matrix (PWM)	0.72	0.73	0.73	0.42	0.82
	Position specific scoring matrix (PSSM)	0.66	0.68	0.67	0.32	0.73
	BLOSUM62 (B62)	0.61	0.58	0.59	0.15	0.60

ISSN: 1752-0509