Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction. (April 2018)

• Record Type: Journal Article
• Authors: Hao, Xiaohu; Zhang, Guijun; Zhou, Xiaogen
• Is Part Of: Computational biology and chemistry. Volume 73(2018)
• Page Start: 105
• Page End: 119
• Publication Date: 2018-04
• Subjects: Ab-initio -- Lipschitz underestimation -- Rosetta -- Differential evolution -- Fragment assembly; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2018.02.003
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: A plug-in method for guiding exploring in conformational space with Lipschitz underestimation for PSP is proposed. The constructed lower bound estimate information can be used for exploration guidance. The invalid sampling areas can be eliminated in advance. The number of energy function evaluations can be reduced. Test on 15 target proteins verify the effectiveness of the proposed method. Abstract: Computing conformations which are essential to associate structural and functional information with gene sequences, is challenging due to the high dimensionality and rugged energy surface of the protein conformational space. Consequently, the dimension of the protein conformational space should be reduced to a proper level, and an effective exploring algorithm should be proposed. In this paper, a plug-in method for guiding exploration in conformational feature space with Lipschitz underestimation (LUE) for ab-initio protein structure prediction is proposed. The conformational space is converted into ultrafast shape recognition (USR) feature space firstly. Based on the USR feature space, the conformational space can be further converted into Underestimation space according to Lipschitz estimation theory for guiding exploration. As a consequence of the use of underestimation model, the tight lower bound estimate information can be used for exploration guidance, the invalid sampling areas can be eliminated in advance, and the number of energy function evaluations can be reduced. The proposed method provides a novel technique to solve the exploring problem of protein conformational space. LUE is applied to differential evolution (DE) algorithm, and metropolis Monte Carlo(MMC) algorithm which is available in the Rosetta; When LUE is applied to DE and MMC, it will be screened by the underestimation method prior to energy calculation and selection. Further, LUE is compared with DE and MMC by testing on 15 small-to-medium structurally diverse proteins. Test results show that near-native protein structures with higher accuracy can be obtained more rapidly and efficiently with the use of LUE.