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Bioinformatics Advance Access originally published online on February 10, 2004
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Bioinformatics 20(8) © Oxford University Press 2004; all rights reserved.

Applications Note

eF-site and PDBjViewer: database and viewer for protein functional sites

Kengo Kinoshita 1,2 and Haruki Nakamura 3,*

1 Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan, 2 Structure and Function of Biomolecules, PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan and 3 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan

Received on September 2, 2003; revised on October 27, 2003; accepted on November 13, 2003
Advance Access Publication February 10, 2004

Summary: The electrostatic-surface of functional site (eF-site) is a database for the molecular surfaces of protein functional sites. To enable browsing of each molecular surface along with the atomic model, we have developed a new three-dimensional interactive viewer, PDBjViewer, that can be used both as an applet and as a stand-alone program.

Availability: The eF-site database and PDBjViewer are freely available from http://www.pdbj.org/eF-site/

Contact: harukin{at}protein.osaka-u.ac.jp

* To whom correspondence should be addressed.


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