Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also occur in de novo design projects guided by molecular docking. To facilitate these processes, there is a need for automated tools capable of efficiently docking a large number of molecules using multiple computational nodes within a reasonable timeframe. These tools should also allow for easy integration of new docking programs and provide a user-friendly program interface to support the development of further approaches utilizing docking as a foundation. Currently available tools have certain limitations, such as lacking a convenient program interface or lacking support for distributed computations. In response to these limitations, we have developed a module called EasyDock. It can be deployed over a network of computational nodes using the Dask library, without requiring a specific cluster scheduler. Furthermore, we have proposed and implemented a simple model that predicts the runtime of docking experiments and applied it to minimize overall docking time. The current version of EasyDock supports popular docking programs, namely Autodock Vina, gnina, and smina. Additionally, we implemented a supplementary feature to enable docking of boron-containing compounds, which are not inherently supported by Vina and smina, and demonstrated its applicability on a set of 55 PDB protein-ligand complexes.

中文翻译：

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EasyDock：可定制和可扩展的对接工具

大型化合物集合的对接成为发现新化学实体的重要程序。大量化合物的筛选也可能发生在分子对接指导下的从头设计项目中。为了促进这些过程，需要能够在合理的时间范围内使用多个计算节点有效对接大量分子的自动化工具。这些工具还应该允许轻松集成新的对接程序，并提供用户友好的程序界面，以支持以对接为基础的进一步方法的开发。目前可用的工具存在一定的局限性，例如缺乏方便的程序接口或缺乏对分布式计算的支持。针对这些限制，我们开发了一个名为 EasyDock 的模块。它可以使用 Dask 库部署在计算节点网络上，而不需要特定的集群调度程序。此外，我们提出并实现了一个简单的模型，可以预测对接实验的运行时间，并应用它来最大限度地减少总体对接时间。当前版本的 EasyDock 支持流行的对接程序，即 Autodock Vina、gnina 和 smina。此外，我们还实现了一项补充功能，以实现 Vina 和 smina 本身不支持的含硼化合物的对接，并证明了其在一组 55 个 PDB 蛋白质-配体复合物上的适用性。