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Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Figure 2

ROC curve showing performance in the large benchmark.

False positive rate (X axis) plotted against true positive rate (Y) for different p-value cut-offs. False positive predictions are defined as those that either have predicted the wrong binding site or have predicted a binding site for a peptide that is not known to bind. The figure shows the result for our approach (pepsite) at two distance thresholds defining accuracy (6 Å & 10 Å), and for 10 Å with a subset of proteins smaller than 100 amino acids. Equivalent values for rate4site on the same datasets are also shown as well as the ROC curve for pepsite using a stricter cross-validation (i.e., excluding similarities/homologies between proteins as given in the SCOP database).

Figure 2