Extended particle swarm optimisation method for folding protein on triangular lattice
文献类型：期刊论文
| 作者 | Guo, Yuzhen1; Wu, Zikai2; Wang, Ying3; Wang, Yong4
|
| 刊名 | IET SYSTEMS BIOLOGY
 |
| 出版日期 | 2016-02-01 |
| 卷号 | 10期号:1页码:30-33 |
| 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 |
| ISSN号 | 1751-8849 |
| DOI | 10.1049/iet-syb.2015.0059 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000370026400006 |
| 出版者 | INST ENGINEERING TECHNOLOGY-IET |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/22099]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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