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. 2004 Jul 1;32(Web Server issue):W545-8.
doi: 10.1093/nar/gkh467.

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

Frédéric Guyon  1 , Anne-Claude Camproux, Joëlle Hochez, Pierre Tufféry
Affiliations

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

Frédéric Guyon et al. Nucleic Acids Res. .

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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Figures

Figure 1
Figure 1
RMSD of the matches as a function of the normalized alignment score. Over 14 000 comparisons are plotted.
Figure 2
Figure 2
Example of a structural match detected using the Smith and Waterman algorithm with gaps. Light: 1aam; Dark: 1c7nA. The two proteins have 10.2% SA sequence identity. The alignment length is 280 residues.
See this image and copyright information in PMC

References

    1. Gibrat J.F., Madej,T. and Bryant,S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377–385. - PubMed
    1. Holm L. and Sander,C. (1993) Protein structure comparison by alignment of distances matrices. J. Mol. Biol., 233, 123–138. - PubMed
    1. Lapthrop R.H. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng., 7, 1059–1068. - PubMed
    1. Shindyalov I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental Combinatorial Extension (CE) of the optimal path. Protein Eng., 11, 739–747. - PubMed
    1. Singh A.P. and Brutlag,D.L. (1997) Hierarchical protein structure alignment using both secondary structure and atomic representations. The Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB-97), 4, Halkidiki, Canada, 284–293. - PubMed