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Nucleic Acids Research 2006 34(Web Server issue):W20-W24; doi:10.1093/nar/gkl267
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

PreBI: prediction of biological interfaces of proteins in crystals

Yuko Tsuchiya1, Kengo Kinoshita2,3,*, Nobutoshi Ito4 and Haruki Nakamura1

1 Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan 2 Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan 3 Structure and Function of Biomolecules, SORST JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan 4 School of Biomedical Science, Tokyo Medical and Dental University 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan

*To whom correspondence should be addressed at Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, 108-8639, Japan. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133; Email: kino{at}ims.u-tokyo.ac.jp

Received February 14, 2006. Revised March 1, 2006. Accepted March 31, 2006.

PreBI is a server that predicts biological interfaces in protein crystal structures, according to the complementarity and the area of the interface. The server accepts a coordinate file in the PDB format, and all of the possible interfaces are generated automatically, according to the symmetry operations given in the coordinate file. For all of the interfaces generated, the complementarities of the electrostatic potential, hydrophobicity and shape of the interfaces are analyzed, and the most probable biological interface is identified according to the combination of the degree of complementarity derived from the database analyses and the area of the interface. The results can be checked through an interactive viewer, and the most probable complex can be downloaded as atomic coordinates in the PDB format. PreBI is available at http://pre-s.protein.osaka-u.ac.jp/~prebi/.


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