Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations

Journal of Computational Chemistry
Yi-yuan ChiuJinn-Moon Yang

Abstract

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...Continue Reading

References

Feb 1, 1992·Protein Science : a Publication of the Protein Society·L Wesson, D Eisenberg
May 5, 1992·Journal of Molecular Biology·L Holm, C Sander
Jan 16, 1986·Nature·D Eisenberg, A D McLachlan
Jul 20, 1973·Science·C B Anfinsen
Apr 1, 1995·Current Opinion in Structural Biology·M J Sippl
Apr 1, 1997·Current Opinion in Structural Biology·S VajdaJ Novotny
May 14, 1999·Current Opinion in Structural Biology·M H Hao, H A Scheraga
Aug 10, 2000·Protein Science : a Publication of the Protein Society·R Samudrala, M Levitt
Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·D KiharaJ Skolnick
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Juan Fernández-RecioRuben Abagyan
Jul 13, 2002·Journal of Computational Chemistry·Daniel J Price, Charles L Brooks
Jul 27, 2002·Protein Science : a Publication of the Protein Society·Jinn-Moon YangCheng-Yan Kao
Aug 7, 2002·Current Opinion in Structural Biology·William P Russ, Rama Ranganathan
Jun 26, 2003·Nucleic Acids Research·Torsten SchwedeManuel C Peitsch
Aug 20, 2003·Journal of Computational Chemistry·Richard D TaylorJonathan W Essex
Oct 28, 2003·Proteins·Björn WallnerArne Elofsson
Jan 6, 2004·Proteins·Yoshimi FujitsukaPeter G Wolynes
Mar 11, 2004·Journal of Computational Chemistry·Jinn-Moon Yang
Mar 30, 2004·Proteins·Jinn-Moon Yang, Chun-Chen Chen
Jun 26, 2004·Bioinformatics·Changyu HuJie Liang
Feb 19, 2005·Current Opinion in Structural Biology·Patrick AloyRobert B Russell
Jul 28, 2005·Journal of Chemical Information and Modeling·Jinn-Moon YangD Frank Hsu
Jul 18, 2006·Nucleic Acids Research·Chih-Chieh ChenJinn-Moon Yang
Feb 9, 2007·Proteins·A BhattacharyayF Seno

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