Department of Physics, University of York, Heslington, York, UK.
Methods Mol Biol. 2022;2476:95-109. doi: 10.1007/978-1-0716-2221-6_8.
Atomic-level computer simulations are a very useful tool for describing the structure and dynamics of complex biomolecules such as DNA and for providing detail at a resolution where experimental techniques cannot arrive. Molecular dynamics (MD) simulations of mechanically distorted DNA caused by agents like supercoiling and protein binding are computationally challenging due to the large size of the associated systems and timescales. However, nowadays they are achievable thanks to the efficient usage of GPU and to the improvements of continuum solvation models. This together with the concurrent improvements in the resolution of single-molecule experiments, such as atomic force microscopy (AFM), makes possible the convergence between the two. Here we present detailed protocols for doing so: for performing molecular dynamics (MD) simulations of DNA adopting complex three-dimensional arrangements and for comparing the outcome of the calculations with single-molecule experimental data with a lower resolution than atomic.
原子级别的计算机模拟是一种非常有用的工具，可用于描述 DNA 等复杂生物分子的结构和动态，并提供实验技术无法达到的分辨率的细节。由于相关系统的规模大和时间尺度大，由超螺旋和蛋白质结合等因素引起的机械扭曲 DNA 的分子动力学（MD）模拟在计算上具有挑战性。然而，如今由于高效使用 GPU 和连续改进连续溶剂模型，它们是可行的。这与单分子实验分辨率的提高（如原子力显微镜（AFM））相结合，使得两者之间有可能实现收敛。在这里，我们提供了执行以下操作的详细方案：对采用复杂三维排列的 DNA 进行分子动力学（MD）模拟，并将计算结果与单分子实验数据进行比较，其分辨率低于原子分辨率。
