Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties

Table 2 The properties and performance of two test datasets: a balanced dataset and whole benchmarking dataset

	TEST SET	BALANCED		BENCHMARKING
TRAINING SET PARAMETERS	Number of catalytic residues	$254 \times \frac{9}{10} *$	$254 \times \frac{9}{10} *$	254	254
	Catalytic vs. Non-catalytic Ratio	1:1	1:1	1:1	1:1
	Number of attributes used	24	7	24	7
TEST SET PARAMETERS	Number of catalytic residues	$254 \times \frac{1}{10} *$	$254 \times \frac{1}{10} *$	254	254
	Catalytic vs. Non-catalytic Ratio	1:1	1:1	1:92	1:92
	Number of attributes used	24	7	24	7
PERFORMANCE	*Accuracy, %*	86.38	87.42	86.68	86.96
	*TP rate*	0.88	0.89	0.90	0.90
	*FP rate*	0.15	0.14	0.13	0.13
	*MCC*	0.73	0.75	0.23	0.23

*- number of catalytic residues in each fold in 10-fold cross- validation analysis

ISSN: 1471-2105