Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Methods Mol Biol. 2023;2552:101-107. doi: 10.1007/978-1-0716-2609-2_4.
Molecular dynamics (MD) simulation is a computational method which elucidates the protein dynamics. Following analyses characterize the dynamics and structural change as well as interaction energy. To characterize the protein structure effectively, the internal angular coordinates are often useful. Directional analysis provides the averages and variances of those coordinates in a mathematically rigorous way. Here, we describe not only a standard MD simulation procedure for the antigen-antibody system but also an umbrella sampling method following a multistep targeted MD simulation (US/mTMD), which is useful for evaluating the free energy profile along the antigen-antibody dissociation coordinate.
分子动力学（MD）模拟是一种阐明蛋白质动力学的计算方法。以下分析可以描述动力学和结构变化以及相互作用能。为了有效地描述蛋白质结构，内部角度坐标通常是有用的。方向分析以数学上严格的方式提供这些坐标的平均值和方差。在这里，我们不仅描述了抗原-抗体系统的标准 MD 模拟程序，还描述了多步靶向 MD 模拟（US/mTMD）之后的伞状采样方法（US/mTMD），该方法可用于评估沿着抗原-抗体解离坐标的自由能分布。
