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Nucleic Acids Research, 2003, Vol. 31, No. 13 3709-3711
© 2003 Oxford University Press

iSPOT: a web tool to infer the interaction specificity of families of protein modules

Barbara Brannetti and Manuela Helmer-Citterich*

Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy

*To whom correpondence should be addressed. Tel: +39 06 72594314; Fax: +39 06 2023500; Email: citterich{at}uniroma2.it

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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