Dixit M, Das S, Mhashal A R, Eitan R, Major D T
Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat Gan, Israel.
Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat Gan, Israel.
Methods Enzymol. 2016;577:251-86. doi: 10.1016/bs.mie.2016.05.046. Epub 2016 Jul 1.
This chapter aims to present some basic multiscale approaches available for enzyme simulations, and to point out practical details and pitfalls that are not often discussed in the literature, but can greatly influence the outcome of any in silico enzyme study. We cover principle methodological steps of multiscale studies of general enzyme reactions. This includes choice of starting structures, boundary conditions, potential energy surfaces, reaction coordinates, simulation methods, as well as the choice of method for the treatment of nuclear quantum effects. Together, these and additional steps are crucial for the success of enzyme-modeling projects and should be considered prior to embarking on multiscale modeling.
本章旨在介绍一些可用于酶模拟的基本多尺度方法，并指出文献中不常讨论但可能极大影响任何计算机酶学研究结果的实际细节和陷阱。我们涵盖了一般酶反应多尺度研究的主要方法步骤。这包括起始结构的选择、边界条件、势能面、反应坐标、模拟方法，以及处理核量子效应的方法选择。这些步骤以及其他步骤共同对酶建模项目的成功至关重要，在着手进行多尺度建模之前应予以考虑。
