Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening,Journal of Computational Chemistry

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Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2025-03-11 , DOI: 10.1002/jcc.70074
Andreas Vitalis ₁ , David Parker ₁ , Fabian Radler ₁ , Pablo A Vargas-Rosales ₁ , Yang Zhang ₁ , Jean-Rémy Marchand ₁ , Amedeo Caflisch ₁

Affiliation

We introduce a software package, ParaLig, that provides solutions for several workflows occurring repeatedly in computational drug discovery: parameterization of small molecules with partial charges and free energies of solvation, generation of conformers, virtual chemical reactions, creating combinatorial libraries, and molecule editing tasks. Throughout, we emphasize the maintenance/creation of 3D coordinates and better interoperability. The latter is achieved by stable embedding of meta‐information into output files and by improving the mutual compatibility of molecular representations (e.g., aromaticity perception). ParaLig wraps around core functionalities provided by a variety of existing software: the two popular cheminformatics packages OpenBabel and RDKit, and the general force field providers CGenFF and AmberTools. Our workflows emphasize scalable bulk processing of large libraries of molecules, and we provide an MPI‐based wrapper to simplify deployment to high‐performance computing resources. Along with salient descriptions of the methods, we benchmark performance both in terms of throughput and in terms of the quality of some of the results.

中文翻译：

用于制备和管理用于虚拟筛选的大型文库的并行化工具

我们推出了一个软件包 ParaLig，它为计算药物发现中反复发生的几个工作流程提供了解决方案：具有部分电荷和溶剂化自由能的小分子参数化、构象异构体的生成、虚拟化学反应、创建组合库和分子编辑任务。自始至终，我们都强调 3D 坐标的维护/创建和更好的互作性。后者是通过将元信息稳定嵌入到输出文件中并通过提高分子表示的相互兼容性（例如，芳香性感知）来实现的。ParaLig 包含各种现有软件提供的核心功能：两个流行的化学信息学软件包 OpenBabel 和 RDKit，以及通用力场提供商 CGenFF 和 AmberTools。我们的工作流程强调对大型分子库的可扩展批量处理，并提供基于 MPI 的包装器，以简化向高性能计算资源的部署。除了对方法的突出描述外，我们还在吞吐量和一些结果的质量方面对性能进行了基准测试。

更新日期：2025-03-11

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