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Bioinformatics Advance Access originally published online on November 8, 2005
Bioinformatics 2006 22(2):188-194; 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{at}oxfordjournals.org

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

Wei Xie and Nikolaos V. Sahinidis *

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.

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 1–10% 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 2–78 times faster than SCWRL 3.0, which is widely used for solving these problems.

Availability: The implementation is available as an online server at http://eudoxus.scs.uiuc.edu/r3.html

Contact: nikos{at}uiuc.edu

Received on August 11, 2005; revised on October 28, 2005; accepted on November 3, 2005

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