Accurate Prediction of Peptide Binding Sites on Protein Surfaces
(A) A training dataset of protein–peptide complexes is extracted from the Protein Data Bank . (B) The peptide residues are superimposed along with their associated binding environments. (C) Spatial Position Specific Scoring Matrices (S-PSSMs) are created based on the spatial distribution of 14 defined atom types (Table S3) in the binding site of each residue. compared to background protein surfaces sites (D) S-PSSMs corresponding to residues in a query peptide (FxPRD) are then scanned over the surface of the protein. (E) Potential binding sites for each residue of the query peptide are identified, which are then combined using the distance constraints dictated by the peptide sequence. (F) The binding site for the complete peptide is predicted and scored.