标题： 采用复制交换溶质温度法对内在无序蛋白进行全原子分子动力学模拟 显示英文标题

标题： Performing all-atom molecular dynamics simulations of intrinsically disordered proteins with replica exchange solute tempering

摘要： 全原子分子动力学（MD）计算机模拟是表征内在无序蛋白（IDP）构象集合的宝贵工具。 IDP的构象集合高度异质，并包含许多具有明显不同拓扑结构且由巨大自由能障碍分隔的结构。 在显式溶剂全原子MD模拟中对IDP的巨大构象空间进行采样极具挑战性，通常需要增强采样方法以获得对IDP构象集合具有统计意义的描述。 复制交换溶质升温（REST）方法是一种有效采样IDP构象空间的强大方法，其中系统进行多组耦合模拟，同时使用选择性修改的势能函数。 在本章中，我们将展示如何使用REST增强采样方法设置、执行和分析IDP的全原子MD模拟。 显示英文摘要

摘要： All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain structures with many distinct topologies separated by large free-energy barriers. Sampling the vast conformational space of IDPs in explicit solvent all-atom MD simulations is extremely challenging, and enhanced sampling methods are generally required to obtain statistically meaningful descriptions of IDP conformational ensembles. Replica exchange solute tempering (REST) methods, where multiple coupled simulations of a system are performed in parallel with selectively modified potential energy functions, are a powerful approach for efficiently sampling the conformational space of IDPs. In this chapter, we demonstrate how to set-up, perform and analyze all-atom MD simulations of IDPs with REST enhanced sampling methods.