This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics, a structured, reproducible and transparent process. In this tutorial we focus on 3 questions: How are protein-ligand systems parameterized for molecular dynamics simulation? What kind of analysis can be carried out on molecular trajectories? How can high-throughput MD be used to study multiple ligands? After finishing you will have learned about force-fields and MD parameterization, how to conduct MD simulation and analysis for a protein-ligand system, and understand how different molecular interactions contribute to the binding affinity of ligands to the Hsp90 protein.

中文翻译：

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Galaxy中直观，可重现的高通量分子动力学：教程

本文是为数据分析平台Galaxy开发的教程。Galaxy的目的是进行高通量的计算数据分析，例如分子动力学，结构化，可再现和透明的过程。在本教程中，我们重点关注3个问题：如何为分子动力学模拟对蛋白质-配体系统进行参数化？可以对分子轨迹进行哪种分析？高通量MD如何用于研究多种配体？完成后，您将了解力场和MD参数化，如何对蛋白质-配体系统进行MD模拟和分析，并了解不同的分子相互作用如何促进配体与Hsp90蛋白质的结合亲和力。