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Nucleic Acids Research 2005 33(Web Server Issue):W331-W336; doi:10.1093/nar/gki585
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© The Author 2005. 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{at}oupjournals.org

Article

PRISM: protein interactions by structural matching

Utkan Ogmen, Ozlem Keskin*, A. Selim Aytuna, Ruth Nussinov1,2 and Attila Gursoy

Koc University, Center for Computational Biology and Bioinformatics and College of Engineering Rumelifeneri Yolu, Sariyer, Istanbul 34450, Turkey 1Basic Research Program, Science Applications International Corporation (SAIC)–Frederick, Inc., LECB, NCI–Frederick Frederick, MD 21702, USA 2Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University Tel Aviv 69978, Israel

*To whom correspondence should be addressed. Tel: +90 212 338 1538; Fax: +90 212 338 1548; Email: okeskin{at}ku.edu.tr

Received February 16, 2005. Revised April 18, 2005. Accepted May 2, 2005.

Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein–protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein–protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution (January 2004). Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.

Correspondence may also be addressed to Attila Gursoy. Tel: +90 212 338 1720; Fax: +90 212 338 1548; Email: agursoy{at}ku.edu.tr


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