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Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations
Author(s) -
Chiu Yiyuan,
Hwang Jennkang,
Yang Jinnmoon
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20897
Subject(s) - benchmark (surveying) , decoy , statistical potential , protein structure prediction , computer science , function (biology) , rank (graph theory) , van der waals force , protein structure , simple (philosophy) , ranking (information retrieval) , biological system , artificial intelligence , chemistry , mathematics , biology , combinatorics , evolutionary biology , molecule , biochemistry , philosophy , receptor , geodesy , organic chemistry , epistemology , geography
We have developed a soft energy function, termed GEMSCORE, for the protein structure prediction, which is one of emergent issues in the computational biology. The GEMSORE consists of the van der Waals, the hydrogen‐bonding potential and the solvent potential with 12 parameters which are optimized by using a generic evolutionary method. The GEMSCORE is able to successfully identify 86 native proteins among 96 target proteins on six decoy sets from more 70,000 near‐native structures. For these six benchmark datasets, the predictive performance of the GEMSCORE, based on native structure ranking and Z ‐scores, was superior to eight other energy functions. Our method is based solely on a simple and linear function and thus is considerably faster than other methods that rely on the additional complex calculations. In addition, the GEMSCORE recognized 17 and 2 native structures as the first and the second rank, respectively, among 21 targets in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction). These results suggest that the GEMSCORE is fast and performs well to discriminate between native and nonnative structures from thousands of protein structure candidates. We believe that GEMSCORE is robust and should be a useful energy function for the protein structure prediction. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008

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