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Bioinformatics Advance Access originally published online on April 15, 2004
Bioinformatics 2004 20(15):2333-2344; doi:10.1093/bioinformatics/bth244
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.

SAD—a normalized structural alignment database: improving sequence–structure alignments

Brian Marsden * and Ruben Abagyan

The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA

Received on August 24, 2003; revised on February 17, 2004; accepted on March 24, 2004
Advance Access Publication April 15, 2004

Motivation: We present a structural alignment database that is specifically targeted for use in derivation and optimization of sequence–structure alignment algorithms for homology modeling. We have paid attention to ensure that fold-space is properly sampled, that the structures involved in alignments are of significant resolution (better than 2.5 Å) and the alignments are accurate and reliable.

Results: Alignments have been taken from the HOMSTRAD, BAliBASE and SCOP-based Gerstein databases along with alignments generated by a global structural alignment method described here. In order to discriminate between equivalent alignments from these different sources, we have developed a novel scoring function, Contact Alignment Quality score, which evaluates trial alignments by their statistical significance combined with their ability to reproduce conserved three-dimensional residue contacts. The resulting non-redundant, unbiased database contains 1927 alignments from across fold-space with high-resolution structures and a wide range of sequence identities.

Availability: The database can be interactively queried either over the web at http://abagyan.scripps.edu/lab/web/sad/show.cgi or by using MySQL, and is also available to download over the web.

Contact: marsden{at}scripps.edu

* To whom correspondence should be addressed.


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