使用Metainference同时测定蛋白质结构和动力学的实用指南
A practical guide to the simultaneous determination of protein structure and dynamics using metainference
摘要：
精确的蛋白质结构系综可以用元参比来确定，元参比是一种贝叶斯推断方法，它将实验信息与系统的先验知识相结合，并处理所有来源的不确定性和误差以及系统异质性。此外，元推理可以使用元自洽方法来实现，这使得需要大量构象采样的复杂生物系统的计算研究成为可能。在本章中，我们提供了一个使用开源PLUMED库的ISDB模块执行和分析元自组织元会议模拟的分步指南，以及一系列避免常见错误的实用技巧。具体来说，我们将指导读者学习如何通过结合最先进的分子力学力场与核磁共振数据，包括化学位移，标量耦合和残余偶极耦合，来模拟小无序肽的结构系综。
英文摘要：
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformational sampling. In this chapter, we provide a step-by-step guide to perform and analyse metadynamic metainference simulations using the ISDB module of the open-source PLUMED library, as well as a series of practical tips to avoid common mistakes. Specifically, we will guide the reader in the process of learning how to model the structural ensemble of a small disordered peptide by combining state-of-the-art molecular mechanics force fields with nuclear magnetic resonance data, including chemical shifts, scalar couplings and residual dipolar couplings.
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