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Nucleic Acids Research 2005 33(Web Server Issue):W337-W341; doi:10.1093/nar/gki482
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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

SiteEngines: recognition and comparison of binding sites and protein–protein interfaces

Alexandra Shulman-Peleg*, Ruth Nussinov1,2 and Haim J. Wolfson

School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University Tel Aviv 69978, Israel 1Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University Tel Aviv 69978, Israel 2Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology NCI-Frederick Building 469, Room 151, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +972 3 6405395; Fax: +972 3 6406476; Email: shulmana{at}tau.ac.il

Received February 14, 2005. Revised April 4, 2005. Accepted April 18, 2005.

Protein surface regions with similar physicochemical properties and shapes may perform similar functions and bind similar binding partners. Here we present two web servers and software packages for recognition of the similarity of binding sites and interfaces. Both methods recognize local geometrical and physicochemical similarity, which can be present even in the absence of overall sequence or fold similarity. The first method, SiteEngine (http:/bioinfo3d.cs.tau.ac.il/SiteEngine), receives as an input two protein structures and searches the complete surface of one protein for regions similar to the binding site of the other. The second, Interface-to-Interface (I2I)-SiteEngine (http:/bioinfo3d.cs.tau.ac.il/I2I-SiteEngine), compares protein–protein interfaces, which are regions of interaction between two protein molecules. It receives as an input two structures of protein–protein complexes, extracts the interfaces and finds the three-dimensional transformation that maximizes the similarity between two pairs of interacting binding sites. The output of both servers consists of a superimposition in PDB file format and a list of physicochemical properties shared by the compared entities. The methods are highly efficient and the freely available software packages are suitable for large-scale database searches of the entire PDB.


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