Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina.
Methods Mol Biol. 2024;2741:207-238. doi: 10.1007/978-1-0716-3565-0_12.
Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many applications to the study of RNA also exist, and their number increases by the day. However, implementing MD simulations for RNA molecules in solution faces challenges that the MD practitioner must be aware of for the appropriate use of this tool. In this chapter, we present the fundamentals of MD simulations, in general, and the peculiarities of RNA simulations, in particular. We discuss the strengths and limitations of the technique and provide examples of its application to elucidate small RNA's performance.
分子动力学模拟已被证明在研究具有原子分辨率的蛋白质功能方面非常有用。也存在许多针对 RNA 研究的应用，并且这个数字每天都在增加。然而，在溶液中对 RNA 分子进行 MD 模拟面临着一些挑战，MD 实践者必须了解这些挑战，才能正确使用该工具。在本章中，我们介绍了 MD 模拟的一般原理，以及 RNA 模拟的特点。我们讨论了该技术的优缺点，并提供了一些应用实例，以阐明小 RNA 的性能。
