Article
Improving the orientation-dependent statistical potential using a reference state
Yufeng Liu,
Jianyang Zeng,
Haipeng Gong,
Yufeng Liu
MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
Search for more papers by this authorJianyang Zeng
Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084 China
Search for more papers by this authorCorresponding Author
Haipeng Gong
MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
Correspondence to: Haipeng Gong; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China. E-mail: [email protected]Search for more papers by this authorYufeng Liu,
Jianyang Zeng,
Haipeng Gong,
Yufeng Liu
MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
Search for more papers by this authorJianyang Zeng
Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084 China
Search for more papers by this authorCorresponding Author
Haipeng Gong
MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
Correspondence to: Haipeng Gong; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China. E-mail: [email protected]Search for more papers by this authorABSTRACT
Statistical potentials are frequently engaged in the protein structural prediction and protein folding for conformational evaluation. Theoretically, to describe the many-body effect, pairwise interaction between two atom groups should be corrected by their relative geometric orientation. The potential functions developed by this means are called orientation-dependent statistical potentials and have exhibited substantially improved performance. However, none of the currently available orientation-dependent statistical potentials use any reference state, which has been proven to greatly enhance the power of distance-dependent statistical potentials in numerous previous studies. In this work, we designed a reasonable reference state for the orientation-dependent statistical potentials: using the average geometric relationship between atom pairs in known structures by neglecting their residue identities. The statistical potential developed using this reference state (called ORDER_AVE) prevails most available rival potentials in a series of tests on the decoy sets, although the information of side chain atoms (except the β-carbon) is absent in its construction. Proteins 2014; 82:2383–2393. © 2014 Wiley Periodicals, Inc.
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