PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W221-6. doi: 10.1093/nar/gku404. Epub 2014 May 6.


Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • DNA Helicases / chemistry
  • DNA Helicases / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Internet
  • Molecular Docking Simulation / methods*
  • Peptides / chemistry*
  • Peptides / metabolism*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Software*


  • DNA-Binding Proteins
  • Peptides
  • Proteins
  • DNA Helicases

Associated data

  • PDB/4NL8