The RCSB Protein Data Bank: redesigned web site and web services

Peter W Rose; Bojan Beran; Chunxiao Bi; Wolfgang F Bluhm; Dimitris Dimitropoulos; David S Goodsell; Andreas Prlić; Martha Quesada; Gregory B Quinn; John D Westbrook; Jasmine Young; Benjamin Yukich; Christine Zardecki; Helen M Berman; Philip E Bourne

doi:10.1093/nar/gkq1021

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The RCSB Protein Data Bank: redesigned web site and web services

Journal article

Open access

Peer reviewed

The RCSB Protein Data Bank: redesigned web site and web services

Peter W Rose, Bojan Beran, Chunxiao Bi, Wolfgang F Bluhm, Dimitris Dimitropoulos, David S Goodsell, Andreas Prlić, Martha Quesada, Gregory B Quinn, John D Westbrook, …

Nucleic acids research, Vol.39(Database issue), pp.D392-D401

01/2011

DOI: https://doi.org/10.1093/nar/gkq1021

PMCID: PMC3013649

PMID: 21036868

Abstract

The RCSB Protein Data Bank (RCSB PDB) web site ( http://www.pdb.org ) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.

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Title: The RCSB Protein Data Bank: redesigned web site and web services
Creators: Peter W Rose - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Bojan Beran - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Chunxiao Bi - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Wolfgang F Bluhm - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Dimitris Dimitropoulos - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
David S Goodsell - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Andreas Prlić - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Martha Quesada - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Gregory B Quinn - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
John D Westbrook - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Jasmine Young - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Benjamin Yukich - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Christine Zardecki - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Helen M Berman - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Philip E Bourne - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093-0743
Publication Details: Nucleic acids research, Vol.39(Database issue), pp.D392-D401
Date published: 01/2011
Publisher: Oxford University Press
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine
Language: English
Resource Type: Journal article
Identifiers: 991031666136804646