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

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

Author information

1
INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
2
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.
3
Technische Universität München 80333 München, Germany.
4
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.

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.

PMID:
24803671
PMCID:
PMC4086095
DOI:
10.1093/nar/gku404
[Indexed for MEDLINE]
Free PMC Article

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