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.

中文翻译：

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StreaMD：高通量分子动力学模拟工具包


分子动力学模拟是研究蛋白质和蛋白质-配体复合物动态行为的常用方法。由于其多功能性和速度，GROMACS 成为执行分子动力学模拟的常用软件平台。然而，它的有效利用需要配置、执行和解释分子动力学轨迹方面的大量专业知识。现有的自动化工具在以最少的用户干预对大量化合物进行模拟的能力或在多个服务器之间分配模拟的能力方面受到限制。为了应对这些挑战，我们开发了一种基于 Python 的工具，可以简化分子动力学模拟的所有阶段，包括准备、执行和分析。该工具最大限度地减少了用户参与分子动力学模拟所需的知识，并且可以在网络或集群内的多个服务器上高效运行。值得注意的是，该工具不仅可以自动化轨迹模拟，还可以促进蛋白质-配体复合物的自由结合能的计算，并在整个轨迹中生成相互作用指纹。我们的研究表明了该工具在多个基准数据集上的适用性。此外，我们还为最终用户提供了有效利用该工具的建议。科学贡献开发的工具 StreaMD 适用于不同的系统（蛋白质、配体及其复合物，包括辅助因子），并且需要一些用户知识来设置和运行分子动力学模拟。 StreaMD 的其他功能是与 MM-GBSA/PBSA 结合自由能和蛋白质-配体相互作用指纹的计算无缝集成，以及在分布式环境中运行模拟。所有这些都将有助于常规和大规模的分子动力学模拟。