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- Title
SA-Search: a web tool for protein structure mining based on a Structural Alphabet.
- Authors
Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre
- 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.
- Publication
Nucleic acids research, 2004, Vol 32, Issue Web Server issue, pW545
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gkh467