Optimal HP configurations of proteins by combining local search with elastic net algorithm
文献类型：期刊论文
| 作者 | Guo, Yu-Zhen; Feng, En-Min; Wang, Yong
|
| 刊名 | JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS
 |
| 出版日期 | 2007-04-10 |
| 卷号 | 70期号:3页码:335-340 |
| 关键词 | protein folding problem 2D HP lattice model elastic net algorithm local search method |
| ISSN号 | 0165-022X |
| DOI | 10.1016/j.jbbm.2006.08.001 |
| 英文摘要 | 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. |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics |
| 语种 | 英语 |
| WOS记录号 | WOS:000245426400002 |
| 出版者 | ELSEVIER SCIENCE BV |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/4264]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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