LowModeMD-Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
LowModeMD-Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
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DOI：
10.1021/ci900508k
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发表时间：
2010-05-01
影响因子：
5.6
通讯作者：
Labute, Paul
中科院分区：
文献类型：
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作者：
Labute, Paul
我们提出了一种用于大环和蛋白质环等复杂分子体系构象搜索的方法。该方法的基础是沿着分子动力学轨迹扰动现有构象，使用初始原子速度，动能集中在低频振动模式，然后能量最小化。一种新的切比雪夫多项式滤波器被用来严重抑制随机产生的Maxwell-Boltzmann速度矢量的高频分量。该方法非常有效，即使对于大型系统也是如此；它的实现非常简单，只需要标准的力场能量和梯度评估。几个计算实验的结果表明，该方法能够有效地采样具有非平凡非键相互作用网络的复杂体系的低应变能构象。
We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is based on perturbing an existing conformation along a molecular dynamics trajectory using initial atomic velocities with kinetic energy concentrated on the low-frequency vibrational modes, followed by energy minimization. A novel Chebyshev polynomial filter is used to heavily dampen the high-frequency components of a randomly generated Maxwell-Boltzmann velocity vector. The method is very efficient, even for large systems; it is straightforward to implement and requires only standard force-field energy and gradient evaluations. The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks.