Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
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DOI：
10.1002/prot.22563
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发表时间：
2010-01-01
影响因子：
2.9
通讯作者：
Orozco, Modesto
中科院分区：
文献类型：
--
作者：
Emperador, Agusti;Meyer, Tim;Orozco, Modesto
我们已经应用了所有原子的离散分子动力学（DMD）的基础上的准物理势研究的灵活性的一组扩展的蛋白质原子的MD模拟。该方法使用纯物理势的补充信息的二级结构，尽管它的简单性是能够再现良好的精度在溶液中的蛋白质的动力学。该方法提出了一个明确的改进，相对于粗粒度的方法的基础上的结构潜力，并打开了可能性，探索动态的蛋白质从平衡和跟踪蛋白质与小分子和大分子配体的相互作用引起的构象变化。
We have applied all atoms discrete molecular dynamics (DMD) based on a quasi-physical potential to study the flexibility of an extended set of proteins for which atomistic MD simulations are available. The method uses pure physical potentials supplemented by information on secondary structure and despite its simplicity is able to reproduce with good accuracy the dynamics of proteins in solution. The method presents a clear improvement with respect to coarse-grained methods based on structure potentials and opens the possibility to explore dynamics of proteins out from the equilibrium and to trace conformational changes induced by interaction of proteins with both small and macromolecular ligands.