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Published online before print June 12, 2008, 10.1110/ps.035022.108
Protein Science (2008), 17:1576-1585. Published by Cold Spring Harbor Laboratory Press. 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 Ma1,2

1 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
2 Department of Bioengineering, Rice University, Houston, Texas 77005, USA

(RECEIVED February 20, 2008; FINAL REVISION May 22, 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 {chi} 1 and {chi} 1+2 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 {chi} 1+2 but 0.3 percentage points weaker for overall {chi} 1. 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 runtime that is one or two orders of magnitude shorter. In addition, OPUS-Rota consistently outperforms SCWRL on the Wallner and 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: rotamers; side-chain modeling; structure prediction; high-accuracy refinement


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