Optimal HP configurations of proteins by combining local search with elastic net algorithm

doi:10.1016/j.jbbm.2006.08.001

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	Optimal HP configurations of proteins by combining local search with elastic net algorithm
	Guo, Yu-Zhen ; Feng, En-Min ; Wang, Yong
	2007-04-10
发表期刊	JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS
ISSN	0165-022X
卷号	70 期号:3 页码:335-340
摘要	The prediction of protein conformation from its amino-acid sequence is one of the most prominent problems in computational biology. But it is NP-hard. Here, we focus on an abstraction widely studied of this problem, the two-dimensional hydrophobic-polar protein folding problem (2D HP PFP). Mathematical optimal model of free energy of protein is established. Native conformations are often sought using stochastic sampling methods, but which are slow. The elastic net (EN) algorithm is one of fast deterministic methods as travelling salesman problem (TSP) strategies. However, it cannot be applied directly to protein folding problem, because of fundamental differences in the two types of problems. In this paper, how the 2D HP protein folding problem can be framed in terms of TSP is shown. Combination of the modified elastic net algorithm and novel local search method is adopted to solve this problem. To our knowledge, this is the first application of EN algorithm to 2D HP model. The results indicate that our approach can find more optimal conformations and is simple to implement, computationally efficient and fast. (c) 2006 Elsevier B.V. All rights reserved.
关键词	protein folding problem 2D HP lattice model elastic net algorithm local search method
DOI	10.1016/j.jbbm.2006.08.001
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
WOS类目	Biochemical Research Methods ; Biochemistry & Molecular Biology ; Biophysics
WOS记录号	WOS:000245426400002
出版者	ELSEVIER SCIENCE BV
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/4265
专题	应用数学研究所
通讯作者	Guo, Yu-Zhen
作者单位	1.Dalian Univ Technol, Dept Appl Math, Dalian 116024, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.Osaka Sangyo Univ, Osaka 5748530, Japan
推荐引用方式 GB/T 7714	Guo, Yu-Zhen,Feng, En-Min,Wang, Yong. Optimal HP configurations of proteins by combining local search with elastic net algorithm[J]. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS,2007,70(3):335-340.
APA	Guo, Yu-Zhen,Feng, En-Min,&Wang, Yong.(2007).Optimal HP configurations of proteins by combining local search with elastic net algorithm.JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS,70(3),335-340.
MLA	Guo, Yu-Zhen,et al."Optimal HP configurations of proteins by combining local search with elastic net algorithm".JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 70.3(2007):335-340.