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Bioinformatics. 2010 Dec 1;26(23):2983-5. doi: 10.1093/bioinformatics/btq572. Epub 2010 Oct 10.

Pre-calculated protein structure alignments at the RCSB PDB website.

Author information

  • 1San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505, USA. andreas@sdsc.edu

Abstract

SUMMARY:

With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.

AVAILABILITY AND IMPLEMENTATION:

A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org

CONTACT:

andreas@sdsc.edu; pbourne@ucsd.edu.

PMID:
20937596
[PubMed - indexed for MEDLINE]
PMCID:
PMC3003546
Free PMC Article
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