Center for NonLinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.
Methods Mol Biol. 2022;2376:331-341. doi: 10.1007/978-1-0716-1716-8_18.
This tutorial will provide a practical overview of the use of atomistic simulations to study thermal unfolding of biomolecules, in particular small proteins and RNA oligomers. The tutorial focuses on the use of atomistic, all atom simulations of biomolecules in explicit solvent, to study (reversible) thermal unfolding. The simulation methods described here have also been applied to study biomolecules using implicit solvent and coarse-grained models. We do not intend to provide an up-to-date review of the vast literature of biomolecular dynamics, enhanced sampling methods, force field developments, and applications of these methods. The purpose of this tutorial is to provide basic guidelines into the use of these methods to the starting scientist.
本教程将提供一个实用的概述，介绍如何使用原子模拟来研究生物分子的热变性，特别是小分子蛋白质和 RNA 寡聚物。本教程侧重于使用明溶剂中的原子级、全原子生物分子模拟来研究（可逆）热变性。这里描述的模拟方法也已应用于使用隐溶剂和粗粒模型研究生物分子。我们并不打算对生物分子动力学、增强采样方法、力场发展以及这些方法的应用的大量文献进行最新综述。本教程的目的是为刚开始使用这些方法的科学家提供使用这些方法的基本指南。
