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

TitlePre-calculated protein structure alignments at the RCSB PDB website.
Publication TypeJournal Article
Year of Publication2010
AuthorsPrlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE
JournalBioinformatics
Volume26
Issue23
Pagination2983-5
Date Published2010 Dec 1
ISSN1367-4811
KeywordsAlgorithms, Amino Acid Sequence, Databases, Protein, Internet, Proteins, Software, Structural Homology, Protein, User-Computer Interface
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 [at] sdsc.edu; pbourne [at] ucsd.edu.

DOI10.1093/bioinformatics/btq572
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/20937596?dopt=Abstract
PMCPMC3003546
Alternate TitleBioinformatics
PubMed ID20937596