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Table 2 Topology-to-topology SVM training and test performance using as input the output of the sequence-to-topology SVM. "With" and "Without Structure II" indicates if the predicted secondary structure of the sequence is also included in input or not. LRG and PHAT columns correspond to the substitution matrices used by the sequence-to-topology SVM.

From: Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier

 

Without Structure II

With Structure II

Substitution Matrix

LRGa

PHATb

LRGc

PHATd

Accuracy

91.7

93.6

92.3

94.3

Sensitivity

42.9

64.3

41.1

44.1

Specificity

95.5

95.9

96.4

98.3

Pnon-IPM

95.4

97.1

95.3

95.6

PIPM

44.1

55.7

47.5

67.1

CPM

0.39

0.64

0.40

0.52

  1. a C = 10.0, 1/2 σ2 = 0.1, predictors = segment of 21 residues
  2. b C = 10.0, 1/2 σ2 = 0.1, predictors = segment of 21 residues
  3. c C = 15.0, 1/2 σ2 = 0.1, predictors = segment of 21 residues + corresponding predicted secondary structure
  4. d C = 5.0, 1/2 σ2 = 0.05, predictors = segment of 21 residues + corresponding predicted secondary structure.