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Table 2 Protein complex classification results obtained through classical SVM and LUPI across different features using LOCO cross-validation over the affinity benchmark dataset

From: Learning protein binding affinity using privileged information

 

Input features

 

2-mer

Blosum (Protein)

 

ROC

PR

S r

ROC

PR

S r

 

Classical SVM

 

0.72

0.68

−0.40

0.70

0.63

−0.36

Privileged features

LUPI-SVM

 NIRP

0.76

0.71

−0.47

0.74

0.70

−0.42

 Moal descriptors

0.78

0.73

−0.48

0.75

0.73

−0.43

 Dias descriptors

0.74

0.70

−0.45

0.73

0.69

−0.40

 Blosum (Interface)

0.73

0.69

−0.41

0.73

0.69

−0.42

  1. Bold faced values indicate best performance for each model
  2. ROC Area under the ROC curve, PR Area under the precision-recall curve, Sr Spearman correlation coefficient
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BMC Bioinformatics

ISSN: 1471-2105

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