Table 1.

Sequence-to-topology SVM performance using the LRG and PHAT matrices

	No Positional Weighting		Positional Weighting
Substitution Matrix	LRGa	PHATb	LRGc	PHATd	MLPe
Accuracy	94.0	93.6	93.9	94.3	90.6
Sensitivity	18.3	9.9	28.4	27.2	35.3
Specificity	99.8	100.0	98.9	99.4	94.8
Pnon-IPM	94.1	93.6	94.8	94.7	95.1
PIPM	87.1	94.4	67.0	76.3	34.2
CPM	0.38	0.30	0.41	0.44	0.30

^a C = 5.0, 1/2σ² = 0.03, window size = 21

^b C = 5.0, 1/2σ² = 0.01, window size = 21

^c C = 25.0, 1/2σ² = 0.40, window size = 21 residues

^d C = 5.0, 1/2σ² = 0.10, window size = 21 residues

^e hidden layer size = 16, window size = 15 residues