Literature DB >> 15215446

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

Frédéric Guyon1, Anne-Claude Camproux, Joëlle Hochez, Pierre Tufféry.   

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.

Mesh：

Year:  2004        PMID： 15215446      PMCID： PMC441605          DOI： 10.1093/nar/gkh467

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


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  19 in total

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7.  Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.

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10.  Improving model construction of profile HMMs for remote homology detection through structural alignment.

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