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Nucleic Acids Research 2006 34(Web Server issue):W235-W238; doi:10.1093/nar/gkl163
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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

RosettaDesign server for protein design

Yi Liu and Brian Kuhlman*

Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA

*To whom correspondence should be addressed. Tel: +1 919 843 0188; Fax: +1 919 966 2852; Email: bkuhlman{at}email.unc.edu

Received January 30, 2006. Revised February 22, 2006. Accepted March 20, 2006.

The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of the designed proteins. The simulations are performed using the design module of the Rosetta program (RosettaDesign). RosettaDesign uses Monte Carlo optimization with simulated annealing to search for amino acids that pack well on the target structure and satisfy hydrogen bonding potential. RosettaDesign has been experimentally validated and has been used previously to stabilize naturally occurring proteins and design a novel protein structure.


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