| Heuristic Quasi-physical Algorithm for Protein Structure Prediction |
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| 作者姓名： | 刘景发 黄文奇 |
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| 作者单位： | [1]School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China [2]Department of Mathematics, Hengyang Normal University, Hengyang 421008, China |
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| 基金项目： | The National Natural Science Foundation of China （ No. 10471051 ） and the National Basic Research Program （973） of China （ No. 2004CB318000） |
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| 摘 要： | A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.
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| 关 键 词： | 蛋白质结构预测 三维蛋白质模型 准物理算法 启发法 |
| 文章编号： | 1005-2429（2006）04-0308-07 |
| 收稿时间： | 2005-12-12 |
Heuristic Quasi-physical Algorithm for Protein Structure Prediction |
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| Liu Jingfa,Huang Wenqi.Heuristic Quasi-physical Algorithm for Protein Structure Prediction[J].Journal of Southwest Jiaotong University,2006,14(4):308-314. |
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| Authors: | Liu Jingfa Huang Wenqi |
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| Abstract: | A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enlightened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world,the algorithm finds low energy configurations for a given monomer chain. An "off-trap" strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13 ≤ n ≤ 55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55,the algorithm finds new low energy configurations different from those given in literatures. |
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| Keywords: | Protein structure prediction Three-dimensional protein model Quasi-physical algorithm Heuristics |
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