Abstract Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein–ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing molecular dynamics simulations. However, its effective utilization requires substantial expertise in configuring, executing, and interpreting molecular dynamics trajectories. Existing automation tools are constrained in their capability to conduct simulations for large sets of compounds with minimal user intervention, or in their ability to distribute simulations across multiple servers. To address these challenges, we developed a Python-based tool that streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis. This tool minimizes the required knowledge for users engaging in molecular dynamics simulations and can efficiently operate across multiple servers within a network or a cluster. Notably, the tool not only automates trajectory simulation but also facilitates the computation of free binding energies for protein–ligand complexes and generates interaction fingerprints across the trajectory. Our study demonstrated the applicability of this tool on several benchmark datasets. Additionally, we provided recommendations for end-users to effectively utilize the tool. Scientific contribution The developed tool, StreaMD, is applicable to different systems (proteins, ligands and their complexes including co-factors) and requires a little user knowledge to setup and run molecular dynamics simulations. Other features of StreaMD are seamless integration with calculation of MM-GBSA/PBSA binding free energies and protein-ligand interaction fingerprints, and running of simulations within distributed environments. All these will facilitate routine and massive molecular dynamics simulations.

Aleksandra Ivanova

Olena Mokshyna

Pavel Polishchuk

Journal of Cheminformatics

JOURNAL OF CHEMINFORMATICS 是一本开放获取期刊，发表化学信息学和分子建模各个方面的原始同行评议研究。覆盖范围包括但不限于：化学信息系统、软件和数据库，以及分子建模化学结构表示及其在结构中的应用、化学物质和化学反应数据库的子结构和相似性搜索计算机和分子图形、计算机辅助分子设计、专家系统、QSAR 和数据挖掘技术。

The Journal of Cheminformatics is an open-access journal dedicated to original peer-reviewed research in all aspects of cheminformatics and molecular modeling. Its scope includes, but is not limited to: chemical information systems, software and databases, molecular modeling of chemical structure representations and their applications, substructure and similarity searching in chemical substance and reaction databases, computer and molecular graphics, computer-aided molecular design, expert systems, QSAR (Quantitative Structure-Activity Relationship), and data mining techniques.

《Journal of Cheminformatics》是一本开放获取的期刊，专注于化学信息学和分子建模领域的原创性同行评审研究。期刊的覆盖范围包括但不限于：化学信息系统、软件和数据库，以及分子建模中的化学结构表示及其应用、化学物质和化学反应数据库的子结构和相似性搜索、计算机和分子图形、计算机辅助分子设计、专家系统、QSAR（定量构效关系）和数据挖掘技术。

Category	Quartile
化学	2
化学, 化学综合	2
化学, 计算机信息系统	2
化学, 计算机跨学科应用	3

StreaMD: the toolkit for high-throughput molecular dynamics simulations

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Journal Info

Category	Quartile
COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS	1