State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, China.
J Comput Chem. 2011 Nov 30;32(15):3188-93. doi: 10.1002/jcc.21900. Epub 2011 Aug 27.
Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins. To evaluate vibrational entropy efficiently and accurately, we, here, propose computation schemes based on coarse-grained NMA methods. This can be achieved by rescaling coarse-grained results with a specific factor that is derived on the basis of the linear correlation of protein vibrational entropy between standard NMA and coarse-grained NMA. Our coarse-grained NMA computation schemes can repeat correctly and efficiently the results of standard NMA for large proteins.
标准正态模式分析（NMA）方法能够计算蛋白质的振动熵，但计算量很大，特别是对于大型蛋白质。为了有效地、准确地计算振动熵，我们在这里提出了基于粗粒化 NMA 方法的计算方案。这可以通过用特定因子对粗粒化结果进行缩放来实现，该因子是基于标准 NMA 和粗粒化 NMA 之间蛋白质振动熵的线性相关关系推导出来的。我们的粗粒化 NMA 计算方案可以正确且高效地重复大型蛋白质的标准 NMA 结果。
