Protein dynamics with off-lattice Monte Carlo moves.
Protein dynamics with off-lattice Monte Carlo moves.
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具有晶格外蒙特卡罗运动的蛋白质动力学。
DOI：
10.1103/physreve.53.4221
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发表时间：
1996
期刊：
影响因子：
--
通讯作者：
Ernst
中科院分区：
文献类型：
--
作者：
Daniel Hoffmann;Ernst
介绍了一种用于全原子蛋白质模型动力学模拟的蒙特卡罗方法，以达到常规分子动力学无法达到的长时间。所考虑的自由度是C$\alpha$-原子处的二面体。两个Monte Carlo移动：扭转轴的单一旋转，并在酰胺平面的窗口合作旋转，改变构象的全球和本地，分别。对于局部移动，雅可比行列式用于获得二面角的无偏分布。采用了适合于蛋白质模型的分子动力学能量函数。多肽通过局部移动而不是全局移动折叠成天然样结构。
A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte Carlo moves are used: single rotations about torsion axes, and cooperative rotations in windows of amide planes, changing the conformation globally and locally, respectively. For local moves Jacobians are used to obtain an unbiased distribution of dihedrals. A molecular dynamics energy function adapted to the protein model is employed. A polypeptide is folded into native-like structures by local but not by global moves.