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Published online before print June 12, 2008
Protein Science, DOI: 10.1110/ps.035022.108
 Copyright © 2008 The Protein Society
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OPUS-Rota: A Fast and Accurate Method for Side-chain Modeling

Mingyang Lu1, Athanasios D. Dousis2, and Jianpeng Ma3,4

1 baylor College of Medicine;
2 Rice University;
3 Baylor College of Medicine

(RECEIVED February 20, 2008; ACCEPTED June 4, 2008)

In this paper, we introduce a fast and accurate side-chain modeling method, named OPUS-Rota. In a benchmark comparison with the methods SCWRL, NCN, LGA, SPRUCE, Rosetta, and SCAP, OPUS-Rota is shown to be much faster than all the methods except SCWRL, which is comparably fast. In terms of overall and accuracies, however, OPUS-Rota is 5.4 and 8.8 percentage points better, respectively, than SCWRL. Compared with NCN, which has the best accuracy in the literature, OPUS-Rota is 1.6 percentage points better for overall but 0.3 percentage points weaker for overall . Hence, our algorithm is much more accurate than SCWRL with similar execution speed, and it has accuracy comparable to or better than the most accurate methods in the literature, but with a run time that is one or two orders of magnitude shorter. In addition, OPUS-Rota consistently outperforms SCWRL on the Wallner & Elofsson homology modeling benchmark set when the sequence identity is greater than 40%. We hope that OPUS-Rota will contribute to high-accuracy structure refinement, and the computer program is freely available for academic users.

Keywords: Protein Structure/Folding; Structure; Protein structure prediction

4 E-mail: jpma{at}bcm.tmc.edu


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