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Nucleic Acids Research Advance Access originally published online on April 28, 2008
Nucleic Acids Research 2008 36(Web Server issue):W233-W238; doi:10.1093/nar/gkn216
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W233-W238
© 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.

Articles

The RosettaDock server for local protein–protein docking

Sergey Lyskov1 and Jeffrey J. Gray1,2,*

1Department of Chemical and Biomolecular Engineering and 2Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA

*To whom correspondence should be addressed. Tel: +1 410 516 5313; Fax: +1 410 516 5510; Email: jgray{at}jhu.edu

Received January 31, 2008. Revised March 25, 2008. Accepted April 9, 2008.

The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.


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