Table 3 Number of correct sites identified.

From: Predicting protein-peptide interaction sites using distant protein complexes as structural templates

Method

# protein-peptide interaction sites (maximum recall)

# protein-protein interaction sites

InterPep*

255 (50.7%)

32 (14.2%)

PeptiMap

230 (45.8%)

39 (17.3%)

GalaxyPepDock*

218 (43.4%)

24 (10.6%)

PepSite2**

176 (35.0%)

54 (23.9%)

InterPep-TMonly*

160 (31.9%)

48 (21.2%)

Surf-Cons

118 (23.5%)

32 (14.2%)

Random

54 (10.8%) σ = 5.9

20 (8.8%) σ = 2.6

Total sites

502 (100.0%)

226 (100.0%)

  1. The number of target pairs where the correct peptide-binding site was identified in the top scorer (cluster for InterPep) for the different methods. #protein-peptide interaction sites measures the number of predictions that hit a protein-peptide interaction site, while #protein-protein interaction sites measures the number of predictions that hit a protein-protein interaction site that is an interaction but not the correct protein-peptide interaction site. Random is what would be expected by chance, and was generated by randomly predicting n number of residues on the surface of the protein as interacting, where n is the number of interacting residues in the native structure. Total is the total number of sites in the test set. *For template methods, no templates matching the target with BLAST E < 0.001 were used. **To make sure PepSite2 was not disadvantaged for longer peptides, it was run with a sliding window of size 10 for the whole peptide and the best prediction was chosen.
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