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Nucleic Acids Research 2004 32(Web Server Issue):W545-W548; doi:10.1093/nar/gkh467
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

Frédéric Guyon*, Anne-Claude Camproux, Joëlle Hochez and Pierre Tufféry

Equipe de Bioinformatique Génomique et Moléculaire, INSERM E346, Université Paris 7, Case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France

* To whom correspondence should be addressed. Tel: +33 1 44 27 77 34; Fax: +33 1 43 26 38 30; Email: guyon{at}ebgm.jussieu.fr

Received February 14, 2004; Revised and Accepted April 29, 2004

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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