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Updated: Sep 23, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
iSPOT: A web tool to infer the interaction specificity of families of protein modules
Barbara Brannetti1, Manuela Helmer-Citterich
1Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.
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.
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