{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T16:23:34Z","timestamp":1778775814074,"version":"3.51.4"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2184,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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.<\/jats:p><jats:p>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<\/jats:p><jats:p>Contact: \u00a0andreas@sdsc.edu; pbourne@ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq572","type":"journal-article","created":{"date-parts":[[2010,10,19]],"date-time":"2010-10-19T04:15:50Z","timestamp":1287461750000},"page":"2983-2985","source":"Crossref","is-referenced-by-count":186,"title":["Pre-calculated protein structure alignments at the RCSB PDB website"],"prefix":"10.1093","volume":"26","author":[{"given":"Andreas","family":"Prli\u0107","sequence":"first","affiliation":[{"name":"1 San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505, 2Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, 3Renaissance Computing Institute, University of North Carolina at Chapel Hill, NC 27517, 4Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093 and 5Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Spencer","family":"Bliven","sequence":"additional","affiliation":[{"name":"1 San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505, 2Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, 3Renaissance Computing Institute, University of North Carolina at Chapel Hill, NC 27517, 4Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093 and 5Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743 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