title: Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server.
abstract: Peptide-mediated interactions are of primordial importance to the cell, and the structure of such interaction provides an important starting point for their further characterization. In many cases, the structure of the peptide-protein complex has not been solved by experiment, and modeling tools need to be applied to generate structural models of the interaction. PeptiMap is a protocol that identifies the peptide-binding site when only the structure of the receptor is known, but no information about where the peptide binds is available. This is achieved by mapping the surface for solvents to identify ligand-binding sites, similar in approach to ANCHORMAP in which amino acids are mapped. Peptimap is a free open access web-based server. It can be accessed at http://peptimap.cluspro.org .
authors.affiliation: Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, MA, 02215, USA.
authors.forename: Tanggis
authors.initials: T
authors.lastname: Bohnuud
authors.affiliation: Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA.
authors.forename: George
authors.initials: G
authors.lastname: Jones
authors.affiliation: Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel. oraf@ekmd.huji.ac.il.
authors.forename: Ora
authors.initials: O
authors.lastname: Schueler-Furman
authors.affiliation: Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, MA, 02215, USA. midas@laufercenter.org.|Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA. midas@laufercenter.org.
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D064878:Web Browser
chemical_list: D010446:Peptide Fragments; D011506:Proteins
keywords: Binding site prediction; Peptide mapping; Peptide-protein interactions; Solvent mapping