NAR Molecular Biology Database Collection entry number 809

http://bioinformatics.albany.edu/~dmaps

Guda C.¹, Pal L.R.¹ and Shindyalov I.N.²

¹GenNYsis Center for Excellence in Cancer Genomics and Department of Epidemiology & Biostatistics, University at Albany, State University of New York, One Discovery drive, Rensselaer, NY 12144-3456
²San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA

Contact cguda@albany.edu

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. 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/post-script and JOY/rtf. DMAPS is accessible online at the URL http://bioinformatics.albany.edu/~dmaps.

This work has been supported by the startup funds to CG from the State University of New York at Albany.

Go to the abstract in the NAR 2006 Database Issue.

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