title: PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
abstract: 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 http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder.
authors.affiliation: INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Saladin
authors.affiliation: INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Rey
authors.affiliation: INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Thévenet
authors.affiliation: Technische Universität München 80333 München, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
authors.affiliation: INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
authors.forename: Gautier
authors.initials: G
authors.lastname: Moroy
authors.affiliation: INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France pierre.tuffery@univ-paris-diderot.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Tufféry
mesh_terms: D001665:Binding Sites; D004265:DNA Helicases / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D062105:Molecular Docking Simulation / Q000379:methods*; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; D010455:Peptides; D011506:Proteins; D004265:DNA Helicases