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Nucleic Acids Research 2006 34(Database Issue):D273-D276; doi:10.1093/nar/gkj018
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Nucleic Acids Research, 2006, Vol. 34, Database issue D273-D276
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

DMAPS: a database of multiple alignments for protein structures

Chittibabu Guda*, Lipika R. Pal and Ilya N. Shindyalov1

Gen*NY*sis Center for Excellence in Cancer Genomics and Department of Epidemiology and Biostatistics, University at Albany, State University of New York One Discovery drive, Rensselaer, NY 12144-3456, USA 1San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA

*To whom correspondence should be addressed. Tel: +1 518 591 7155; Fax: +1 518 591 7201; Email: cguda{at}albany.edu

Received August 15, 2005. Accepted September 17, 2005.

The database of multiple alignments for protein structures (DMAPS) provides instant access to pre-computed multiple structure alignments for all protein structure families in the Protein Data Bank (PDB). Protein structure families have been obtained from four distinct classification methods including SCOP, CATH, ENZYME and CE, and multiple structure alignments have been built for all families containing at least three members, using CE-MC software. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. A web-based query system has been developed to retrieve multiple alignments for these families using the PDB chain ID of any member of a family. Multiple alignments can be viewed or downloaded in six different formats, including JOY/html, TEXT, FASTA, PDB (superimposed coordinates), JOY/postscript and JOY/rtf. DMAPS is accessible online at http://bioinformatics.albany.edu/~dmaps.


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[Abstract] [Full Text] [PDF]


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