title: iSPOT: A web tool to infer the interaction specificity of families of protein modules.
abstract: iSPOT (http://cbm.bio.uniroma2.it/ispot) is a web tool developed to infer the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from position-specific contacts, derived from the available domain/ligand complexes of known structure, and experimental interaction data to build a database of residue-residue contact frequencies. iSPOT is available to infer the interaction specificity of PDZ, SH3 and WW domains. For each family of protein domains, iSPOT evaluates the probability of interaction between a query domain of the specified families and an input protein/peptide sequence and makes it possible to search for potential binding partners of a given domain within the SWISS-PROT database. The experimentally derived interaction data utilized to build the PDZ, SH3 and WW databases of residue-residue contact frequencies are also accessible. Here we describe the application to the WW family of protein modules.
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
authors.forename: Barbara
authors.initials: B
authors.lastname: Brannetti
authors.forename: Manuela
authors.initials: M
authors.lastname: Helmer-Citterich
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D020407:Internet; D008024:Ligands; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D018909:src Homology Domains
chemical_list: D008024:Ligands; D011506:Proteins