OPUS-Rota: A fast and accurate method for side-chain modeling

Authors

  • Mingyang Lu,

    1. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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  • Athanasios D. Dousis,

    1. Department of Bioengineering, Rice University, Houston, Texas 77005, USA
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  • Jianpeng Ma

    Corresponding author
    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
    • Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030, USA; fax: (713) 796-9438.
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Abstract

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 χ1 and χ1+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 χ1+2 but 0.3 percentage points weaker for overall χ1. 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.

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