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Bioinformatics Advance Access published online on November 8, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti763
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 11, 2005
Revised October 28, 2005
Accepted November 3, 2005

Article

Residue-rotamer-reduction algorithm for the protein side-chain conformation problem

Wei Xie 1 and Nikolaos V. Sahinidis 1*

1 Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA

* To whom correspondence should be addressed.
Nikolaos V. Sahinidis, E-mail: nikos{at}uiuc.edu


  Abstract

Motivation: The protein side-chain conformation problem is a central problem in proteomics with wide applications in protein structure prediction and design. Computational complexity results show that the problem is hard to solve. Yet, instances from realistic applications are large and demand fast and reliable algorithms.

Results: We propose a new global optimization algorithm which for the first time integrates residue reduction and rotamer reduction techniques previously developed for the protein side-chain conformation problem. We show that the proposed approach simplifies dramatically the topology of the underlining residue graph. Computations show that our algorithm solves problems using only 1 to 10% of the time required by the mixed-integer linear programming approach available in the literature. In addition, on a set of hard side-chain conformation problems, our algorithm runs 2 to 78 times faster than SCWRL 3.0, which is widely used for solving these problems.

Availability: R3 online server at: http://eudoxus.scs.uiuc.edu/r3.html.


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[Abstract] [Full Text] [PDF]


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