Extended particle swarm optimisation method for folding protein on triangular lattice

doi:10.1049/iet-syb.2015.0059

CSpace > 应用数学研究所

	Extended particle swarm optimisation method for folding protein on triangular lattice
	Guo, Yuzhen 1; Wu, Zikai 2; Wang, Ying 3; Wang, Yong4
	2016-02-01
发表期刊	IET SYSTEMS BIOLOGY
ISSN	1751-8849
卷号	10 期号:1 页码:30-33
摘要	In this study, the authors studied the protein structure prediction problem by the two-dimensional hydrophobic-polar model on triangular lattice. Particularly the non-compact conformation was modelled to fold the amino acid sequence into a relatively larger triangular lattice, which is more biologically realistic and significant than the compact conformation. Then protein structure prediction problem was abstracted to match amino acids to lattice points. Mathematically, the problem was formulated as an integer programming and they transformed the biological problem into an optimisation problem. To solve this problem, classical particle swarm optimisation algorithm was extended by the single point adjustment strategy. Compared with square lattice, conformations on triangular lattice are more flexible in several benchmark examples. They further compared the authors' algorithm with hybrid of hill climbing and genetic algorithm. The results showed that their method was more effective in finding solution with lower energy and less running time.
关键词	proteins molecular biophysics molecular configurations particle swarm optimisation bioinformatics extended particle swarm optimisation method triangular lattice protein structure prediction problem two-dimensional hydrophobic-polar model noncompact conformation amino acid sequence single point adjustment strategy protein folding
DOI	10.1049/iet-syb.2015.0059
语种	英语
资助项目	Foundation from Nanjing University of Aeronautics and Astronautics[NN2014083] ; Natural Science Foundation of China[61304178] ; Foundation from Dalian Jiaotong University[L2011068]
WOS研究方向	Cell Biology ; Mathematical & Computational Biology
WOS类目	Cell Biology ; Mathematical & Computational Biology
WOS记录号	WOS:000370026400006
出版者	INST ENGINEERING TECHNOLOGY-IET
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/22100
专题	应用数学研究所
通讯作者	Guo, Yuzhen
作者单位	1.Nanjing Univ Aeronaut & Astronaut, Dept Math, Nanjing, Jiangsu, Peoples R China 2.Univ Shanghai Sci & Technol, Sch Business, Shanghai, Peoples R China 3.Dalian Jiaotong Univ, Sch Sci, Dalian, Peoples R China 4.Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Guo, Yuzhen,Wu, Zikai,Wang, Ying,et al. Extended particle swarm optimisation method for folding protein on triangular lattice[J]. IET SYSTEMS BIOLOGY,2016,10(1):30-33.
APA	Guo, Yuzhen,Wu, Zikai,Wang, Ying,&Wang, Yong.(2016).Extended particle swarm optimisation method for folding protein on triangular lattice.IET SYSTEMS BIOLOGY,10(1),30-33.
MLA	Guo, Yuzhen,et al."Extended particle swarm optimisation method for folding protein on triangular lattice".IET SYSTEMS BIOLOGY 10.1(2016):30-33.