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Nucleic Acids Research Advance Access originally published online on October 4, 2008
Nucleic Acids Research 2009 37(Database issue):D360-D364; doi:10.1093/nar/gkn659
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Nucleic Acids Research, 2009, Vol. 37, Database issue D360-D364
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

PiSite: a database of protein interaction sites using multiple binding states in the PDB

Miho Higurashi1, Takashi Ishida1 and Kengo Kinoshita1,2,*

1Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 and 2Bioinformatics Research and Development, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133; Email: kino{at}ims.u-tokyo.ac.jp

Received August 15, 2008. Revised September 19, 2008. Accepted September 21, 2008.

The vast accumulation of protein structural data has now facilitated the observation of many different complexes in the PDB for the same protein. Therefore, a single protein complex is not sufficient to identify their interaction sites, especially for proteins with multiple binding states or different partners, such as hub proteins. PiSite is a database that provides protein–protein interaction sites at the residue level with consideration of multiple complexes at the same time, by mapping the binding sites of all complexes containing the same protein in the PDB. PiSite provides easy web interfaces with an interactive viewer working with typical web browsers, and the different binding modes can be checked visually. All of the information can also be downloaded for further analyses. In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein–protein interfaces. PiSite is available at http://pisite.hgc.jp

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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