We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy’s graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 50000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.

中文翻译：

---

基于片段的虚拟筛选的 Galaxy 工作流程：SARS-CoV-2 主要蛋白酶的案例研究

我们提出了几个用于蛋白质-配体对接和自由能计算的工作流程，用于工作流程管理系统 Galaxy。工作流程由几个广泛使用的开源工具组成，包括 rDock 和 GROMACS，并且可以使用 Galaxy 的图形界面或命令行在公共基础设施上执行。我们通过针对 SARS-CoV-2 主要蛋白酶对大约 50000 种化合物进行高通量虚拟筛选来展示工作流程的实用性，该系统在去年一直是深入研究的主题。