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Nucleic Acids Research Advance Access originally published online on May 7, 2007
Nucleic Acids Research 2007 35(Web Server issue):W451-W454; doi:10.1093/nar/gkm296
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W451-W454
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

SH3-Hunter: discovery of SH3 domain interaction sites in proteins

Enrico Ferraro*, Daniele Peluso, Allegra Via, Gabriele Ausiello 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 correspondence should be addressed. Tel: +39 06 72594324; Fax: +39 06 72594314; Email: enrico.ferraro{at}uniroma2.it

Received February 1, 2007. Revised April 6, 2007. Accepted April 12, 2007.

SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide–domain pairs. The server can accept a list of peptides and allows users to upload an input file in a proper format. An accurate selection of SH3 domains is available and users can also submit their own SH3 domain sequence.

SH3-Hunter evaluates which peptide–domain pair represents a possible interaction pair and produces as output a list of significant interaction sites for each query protein. Each proposed interaction site is associated to a propensity score and sensitivity and precision levels for the prediction. The server prediction capability is based on a neural network model integrating high-throughput pep-spot data with structural information extracted from known SH3-peptide complexes.


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