| 蛋白质HP模型的改进和PERM算法求解 |
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| 引用本文： | 陈凤飞,黄文奇.蛋白质HP模型的改进和PERM算法求解[J].计算机仿真,2007,24(5):287-290. |
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| 作者姓名： | 陈凤飞 黄文奇 |
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| 作者单位： | 华中科技大学计算机科学与技术学院,武汉,430074 |
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| 基金项目： | 国家重点基础研究发展计划(973计划) |
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| 摘 要： | HP模型是一种被广泛研究的简化的蛋白质折叠模型.在蛋白质螺旋结构的预测上有很高的可信度.但是HP的正方格点模型存在能量计算缺陷,影响其对链上特定结构的计算.针对这一缺陷,给出一种模型上的修正,引入了三角化的格点模型.利用求解格点蛋白质模型高效的算法PERM对通用算例进行了基于2-D三角格点模型的仿真计算.得到了紧密的蛋白质链折叠构型.构型最小能量比正方格点模型更低,得到的标准算例构型比较吻合实际蛋白质折叠的直观构型.计算结果验证了改进模型的有效性.对后续的研究提出了建议.
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| 关 键 词： | 蛋白质折叠 三角化方法 格点模型 算法 人口控制 蛋白质 改进模型 PERM 算法 求解 Solution Protein Folding HP Model 有效性 结果验证 比较 标准 能量比 最小 链折叠 仿真计算 算例 格点模型 利用 三角化 |
| 文章编号： | 1006-9348（2007）05-0287-04 |
| 修稿时间： | 2006-02-272006-04-09 |
2-Dimensional Triangular Lattice HP Model for Protein Folding and a PERM Solution |
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| CHEN feng-fei,HUANG Wen-qi.2-Dimensional Triangular Lattice HP Model for Protein Folding and a PERM Solution[J].Computer Simulation,2007,24(5):287-290. |
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| Authors: | CHEN feng-fei HUANG Wen-qi |
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| Affiliation: | School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan Hubei 430074, China |
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| Abstract: | HP model is the most densely studied abstract model for protein folding. Due to its square lattice based configuration, a defect is inherited which causes an energy calculation deviation for certain sequences inside a protein chain. An elegant and compact remedy is proposed based on HP lattice model and an algorithm which is the most efficient and quickest method for lattice model based protein folding problem is introduced and applied to this improved model. Compact folding configurations with much more lower energies are obtained. The minimum energy acquired is lower than that of square lattice model, which proves the success of the improvement. Successive research trend is proposed. |
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| Keywords: | Protein folding Triangulation Lattice model Algorithm Population control |
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