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Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W545-8.

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

Author information

  • 1Equipe de Bioinformatique Génomique et Moléculaire, INSERM E346, Université Paris 7, Case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France. guyon@ebgm.jussieu.fr

Abstract

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.

PMID:
15215446
[PubMed - indexed for MEDLINE]
PMCID:
PMC441605
Free PMC Article

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