title: PeptiSite: a structural database of peptide binding sites in 4D.
abstract: We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include: (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions and (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://peptisite.ucsd.edu/ link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.
authors.affiliation: UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
authors.forename: Chayan
authors.initials: C
authors.lastname: Acharya
authors.affiliation: UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Kufareva
authors.affiliation: UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russia; Research and Education Center "Biophysics", PNPI and St. Petersburg State Polytechnical University, St. Petersburg 195251, Russia.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Ilatovskiy
authors.affiliation: UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. Electronic address: rabagyan@ucsd.edu.
authors.forename: Ruben
authors.initials: R
authors.lastname: Abagyan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D020134:Catalytic Domain; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000378:metabolism*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins
keywords: Induced-fit; PeptiSite; Peptide binding site; Pocketome; SiteFinder