Quasi-physical Algorithm for Protein Folding in an Off-Lattice Model
Quasi-physical Algorithm for Protein Folding in an Off-Lattice Model
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DOI：
10.1088/0253-6102/47/1/034
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发表时间：
2007-01
影响因子：
3.1
通讯作者：
Lü Zhi-Peng;Huang Wen-qi;S. He
中科院分区：
文献类型：
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作者：
Lü Zhi-Peng;Huang Wen-qi;S. He
我们研究了三维离格蛋白质折叠模型，其中涉及两种残基通过伦纳德-琼斯势相互作用。通过将额外的能量贡献合并到原始势函数中，我们用混合势函数的无约束最小化来代替原始的约束问题。因此，提出了一种解决蛋白质折叠问题的有效准物理算法。我们将所提出的算法应用于最多 55 个残基的序列，并将计算结果与几种最著名的算法发现的假定最低能量进行比较，显示了我们方法的优势。还讨论了准物理算法的动态行为。
We study a three-dimensional off-lattice protein folding model, which involves two species of residues interacting through Lennard–Jones potentials. By incorporating an extra energy contribution into the original potential function, we replace the original constrained problem with an unconstrained minimization of a mixed potential function. As such an efficient quasi-physical algorithm for solving the protein folding problem is presented. We apply the proposed algorithm to sequences with up to 55 residues and compare the computational results with the putative lowest energy found by several of the most famous algorithms, showing the advantages of our method. The dynamic behavior of the quasi-physical algorithm is also discussed.