Energy landscape paving with local search for global optimization of the BLN off-lattice model

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成果类型：

期刊论文

作者：

Liu, Jingfa*;Huang, Weibo;Liu, Wenjie;Song, Beibei;Sun, Yuanyuan;...

通讯作者：

Liu, Jingfa

作者机构：

[Liu, Jingfa] Nanjing Univ Informat Sci & Technol, Network Informat Ctr, Nanjing 210044, Jiangsu, Peoples R China.

[Huang, Weibo; Liu, Jingfa; Liu, Wenjie; Song, Beibei; Sun, Yuanyuan] Nanjing Univ Informat Sci & Technol, Sch Comp & Software, Nanjing 210044, Jiangsu, Peoples R China.

[Huang, Weibo; Liu, Wenjie; Song, Beibei; Sun, Yuanyuan] Nanjing Univ Informat Sci & Technol, Jiangsu Engn Ctr Network Monitoring, Nanjing 210044, Jiangsu, Peoples R China.

[Chen, Mao] Cent China Normal Univ, Natl Engn Res Ctr E Learning, Wuhan 475001, Peoples R China.

通讯机构：

[Liu, Jingfa] N

Nanjing Univ Informat Sci & Technol, Network Informat Ctr, Nanjing 210044, Jiangsu, Peoples R China.

语种：

英文

关键词：

Energy landscape paving method;Global optimization;BLN off-lattice model;Gradient descent method

期刊：

Journal of the Korean Physical Society

ISSN：

0374-4884

年：

2014

卷：

期：

页码：

603-610

DOI：

10.3938/jkps.64.603

基金类别：

This work is supported by the National Natural Science Foundation of China (61373016), the Natural Science Foundation of Jiangsu Province (BK2010570), the National Natural Science Foundation of China (61103235) and its sub-project (20110150-1), the Six Talent Peaks Project of Jiangsu Province (DZXX-041), and the Special Foundation of China Postdoctoral Science Foundation (201104572).

机构署名：

本校为其他机构

院系归属：

国家数字化学习工程技术研究中心

摘要：

The optimization problem for finding the global minimum energy structure is one of the main problems of protein structure prediction and is known to be an NP-hard problem in computational molecular biology. The low-energy conformational search problem in the hydrophobic-hydrophilic-neutral (BLN) off-lattice model is studied. We convert the problem into an unconstrained optimization problem by introducing the penalty function. By putting forward a new updating mechanism of the histogram function in the energy landscape paving (ELP) method and incorporating heuristic conformation update strategi...

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Energy landscape paving with local search for global optimization of the BLN off-lattice model

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