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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 A) 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.

Original publication

DOI

10.1093/bioinformatics/bth244

Type

Journal article

Journal

Bioinformatics

Publication Date

12/10/2004

Volume

20

Pages

2333 - 2344

Keywords

Algorithms, Amino Acid Sequence, Database Management Systems, Databases, Protein, Information Storage and Retrieval, Internet, Models, Molecular, Molecular Sequence Data, Protein Conformation, Proteins, Sequence Alignment, Sequence Analysis, Sequence Homology, Amino Acid