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首页> 外文期刊>PHYSICAL REVIEW E >Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins
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Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins

机译：能量-景观铺装预测面心立方疏水-亲水晶格模型蛋白

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摘要

Protein structure prediction (PSP) is a classical NP-hard problem in computational biology. The energylandscapenpaving (ELP) method is a class of heuristic global optimization algorithm, and has been successfullynapplied to solving many optimization problems with complex energy landscapes in the continuous space. Bynputting forward a new update mechanism of the histogram function in ELP and incorporating the generation ofninitial conformation based on the greedy strategy and the neighborhood search strategy based on pull moves intonELP, an improved energy-landscape paving (ELP+) method is put forward. Twelve general benchmark instancesnare first tested on both two-dimensional and three-dimensional (3D) face-centered-cubic (fcc) hydrophobichydrophilicn(HP) lattice models. The lowest energies by ELP+ are as good as or better than those of othernmethods in the literature for all instances. Then, five sets of larger-scale instances, denoted by S, R, F90, F180,nand CASP target instances on the 3D FCC HP lattice model are tested. The proposed algorithm finds lowernenergies than those by the five other methods in literature. Not unexpectedly, this is particularly pronounced fornthe longer sequences considered. Computational results show that ELP+ is an effective method for PSP on thenfcc HP lattice model.
机译：蛋白质结构预测（PSP）是计算生物学中的经典NP难题。 Energylandscapenpaving（ELP）方法是一类启发式全局优化算法，已成功应用于解决连续空间中具有复杂能量景观的许多优化问题。提出了一种新的ELP直方图函数更新机制，并结合基于贪婪策略的初始构象的生成和基于intonELP的拉动邻域搜索策略的提出，提出了一种改进的能量-景观铺装（ELP +）方法。首先对十二个通用基准实例进行了二维和三维（3D）面心立方（fcc）疏水亲水（HP）晶格模型测试。在所有情况下，ELP +的最低能量与文献中的其他方法一样好或更好。然后，对3D FCC HP晶格模型上的S，R，F90，F180，n和CASP目标实例表示的五组大型实例进行了测试。与文献中的其他五种方法相比，该算法发现的能量更低。毫不意外的是，考虑到更长的序列，这一点尤其明显。计算结果表明，ELP +是在fcc HP晶格模型上进行PSP的有效方法。

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  • 来源
    《PHYSICAL REVIEW E》 |2013年第5期|1-9|共9页
  • 作者

    Jingfa Liu; Beibei Song; Zhaoxia Liu; Weibo Huang; Yuanyuan Sun; Wenjie Liu;

  • 作者单位

    Jiangsu Engineering Center of Network Monitoring Nanjing University of Information Science and Technology Nanjing 210044 ChinaNetwork Information Center Nanjing University of Information Science and Technology Nanjing 210044 China;

    Jiangsu Engineering Center of Network Monitoring Nanjing University of Information Science and Technology Nanjing 210044 ChinaSchool of Computer and Software Nanjing University of Information Science and Technology Nanjing 210044 China;

    Network Information Center Nanjing University of Information Science and Technology Nanjing 210044 China;

    Jiangsu Engineering Center of Network Monitoring Nanjing University of Information Science and Technology Nanjing 210044 ChinaSchool of Computer and Software Nanjing University of Information Science and Technology Nanjing 210044 China;

    Jiangsu Engineering Center of Network Monitoring Nanjing University of Information Science and Technology Nanjing 210044 ChinaSchool of Computer and Software Nanjing University of Information Science and Technology Nanjing 210044 China;

    Jiangsu Engineering Center of Network Monitoring Nanjing University of Information Science and Technology Nanjing 210044 ChinaSchool of Computer and Software Nanjing University of Information Science and Technology Nanjing 210044 China;

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