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Nucleic Acids Research 2005 33(Web Server Issue):W363-W367; doi:10.1093/nar/gki481
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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

PatchDock and SymmDock: servers for rigid and symmetric docking

Dina Schneidman-Duhovny, Yuval Inbar, 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/Fax: +972 3 640 6476; Email: wolfson{at}tau.ac.il

Received February 14, 2005. Revised March 22, 2005. Accepted April 18, 2005.

Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein–protein and protein–small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.

Correspondence may also be addressed to Dina Schneidman-Duhovny. Tel: +972 3 640 5395; Fax: +972 3 640 6476; Email: duhovka{at}tau.ac.il


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