Application of molecular dynamics simulation in biomedicine,Chemical Biology & Drug Design

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Application of molecular dynamics simulation in biomedicine
Chemical Biology & Drug Design ( IF 3.2 ) Pub Date : 2022-03-16 , DOI: 10.1111/cbdd.14038
Xiaodong Wu ₁ , Li‐Yan Xu _{2,

3} , En‐Min Li _{1,

2} , Geng Dong _{1,

4}

Affiliation

Molecular dynamics (MD) simulation has been widely used in the field of biomedicine to study the conformational transition of proteins caused by mutation or ligand binding/unbinding. It provides some perspectives those are difficult to find in traditional biochemical or pathological experiments, for example, detailed effects of mutations on protein structure and protein–protein/ligand interaction at the atomic level. In this review, a broad overview on conformation changes and drug discovery by MD simulation is given. We first discuss the preparation of protein structure for MD simulation, which is a key step that determines the accuracy of the simulation. Then, we summarize the applications of commonly used force fields and MD simulations in scientific research. Finally, enhanced sampling methods and common applications of these methods are introduced. In brief, MD simulation is a powerful tool and it can be used to guide experimental study. The combination of MD simulation and experimental techniques is an a priori means to solve the biomedical problems and give a deep understanding on the relationship between protein structure and function.

中文翻译：

分子动力学模拟在生物医学中的应用

分子动力学（MD）模拟已广泛应用于生物医学领域，以研究由突变或配体结合/解结合引起的蛋白质构象转变。它提供了一些在传统生化或病理学实验中难以发现的观点，例如，突变对蛋白质结构和原子水平蛋白质-蛋白质/配体相互作用的详细影响。在这篇综述中，对通过 MD 模拟的构象变化和药物发现进行了广泛的概述。我们首先讨论了用于 MD 模拟的蛋白质结构的制备，这是决定模拟准确性的关键步骤。然后，我们总结了常用的力场和MD模拟在科学研究中的应用。最后，介绍了增强的采样方法和这些方法的常见应用。简而言之，MD 模拟是一种强大的工具，可以用来指导实验研究。MD模拟与实验技术相结合，是解决生物医学问题、深入理解蛋白质结构与功能关系的先验手段。

更新日期：2022-03-16

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