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Briefings in Bioinformatics Advance Access originally published online on April 22, 2008
Briefings in Bioinformatics 2008 9(4):276-285; doi:10.1093/bib/bbn015
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Protein structure databases with new web services for structural biology and biomedical research

Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita and Haruki Nakamura

Corresponding author. Haruki Nakamura, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan. E-mail: harukin{at}protein.osaka-u.ac.jp

The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes ~25–30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.

Keywords: PDB, functional annotation, molecular surface, structural alignment, protein universe

Submitted: January 11, 2008. Accepted: March 10, 2008.


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