Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling

doi:10.1186/s12859-019-2652-5

CORC > 理论物理研究所 > 中国科学院理论物理研究所 > 理论物理所科研产出 > 理论物理所1978-2010年知识产出

	Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling
	Wang, C ; Wei, Y ; Zhang, HC ; Kong, LP ; Sun, SW ; Zheng, WM ; Bu, DB
刊名	BMC BIOINFORMATICS
	2019
卷号	20 页码:135
关键词	TERTIARY STRUCTURES FRAGMENTS
ISSN号	1471-2105
DOI	10.1186/s12859-019-2652-5
英文摘要	BackgroundThe ab initio approaches to protein structure prediction usually employ the Monte Carlo technique to search the structural conformation that has the lowest energy. However, the widely-used energy functions are usually ineffective for conformation search. How to construct an effective energy function remains a challenging task.ResultsHere, we present a framework to construct effective energy functions for protein structure prediction. Unlike existing energy functions only requiring the native structure to be the lowest one, we attempt to maximize the attraction-basin where the native structure lies in the energy landscape. The underlying rationale is that each energy function determines a specific energy landscape together with a native attraction-basin, and the larger the attraction-basin is, the more likely for the Monte Carlo search procedure to find the native structure. Following this rationale, we constructed effective energy functions as follows: i) To explore the native attraction-basin determined by a certain energy function, we performed reverse Monte Carlo sampling starting from the native structure, identifying the structural conformations on the edge of attraction-basin. ii) To broaden the native attraction-basin, we smoothened the edge points of attraction-basin through tuning weights of energy terms, thus acquiring an improved energy function. Our framework alternates the broadening attraction-basin and reverse sampling steps (thus called BARS) until the native attraction-basin is sufficiently large. We present extensive experimental results to show that using the BARS framework, the constructed energy functions could greatly facilitate protein structure prediction in improving the quality of predicted structures and speeding up conformation search.ConclusionUsing the BARS framework, we constructed effective energy functions for protein structure prediction, which could improve the quality of predicted structures and speed up conformation search as well.
学科主题	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
语种	英语
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/23459]
专题	理论物理研究所_理论物理所1978-2010年知识产出
作者单位	1.Univ Chinese Acad Sci, 19-1 Yuquan Rd, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Inst Theoret Phys, 55 Zhongguancun East Rd, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Inst Comp Technol, 6 Kexueyuan South Rd, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Wang, C,Wei, Y,Zhang, HC,et al. Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling[J]. BMC BIOINFORMATICS,2019,20:135.
APA	Wang, C.,Wei, Y.,Zhang, HC.,Kong, LP.,Sun, SW.,...&Bu, DB.(2019).Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling.BMC BIOINFORMATICS,20,135.
MLA	Wang, C,et al."Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling".BMC BIOINFORMATICS 20(2019):135.