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

Frédéric Guyon·Anne-Claude Camproux·Joëlle Hochez·Pierre Tufféry
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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.

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Amino Acid SequenceInternetMarkov ChainsProtein ConformationSequence AlignmentSoftwareStructural Homology, ProteinJournal Article

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Frédéric Guyon, Anne-Claude Camproux, Joëlle Hochez, Pierre Tufféry. 2004-07-01. SA-Search: a web tool for protein structure mining based on a Structural Alphabet.. https://doi.org/10.1093/nar%2Fgkh467

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