Molecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more. Ideally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols. Here, we introduce MDRepo, a robust infrastructure that provides a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyber-infrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.

中文翻译：

---

MDRepo — 一个开放数据仓库，用于社区贡献的蛋白质分子动力学模拟


生物分子的分子动力学 （MD） 模拟为构象变化和动态行为提供了重要的见解，揭示了有关折叠和与其他分子相互作用的关键信息。存储在世界各地计算机中的模拟集合具有巨大的潜力，可以作为未来机器学习模型的训练数据，这些模型将改变结构、动力学、药物相互作用等的预测。理想情况下，应该有一个开放访问的存储库，使科学家能够提交和存储他们对蛋白质和蛋白质-药物相互作用的 MD 模拟，并查找、检索、分析和可视化其他人生成的模拟。然而，尽管 MD 模拟在结构生物学中无处不在，但不存在这样的存储库;因此，模拟存储在分散的位置，没有统一的元数据或访问协议。在这里，我们介绍了 MDRepo，这是一个强大的基础设施，它为标准化的社区模拟贡献提供了一个相对简单的流程，激活了对存储数据的常见下游分析，并支持对贡献的数据进行搜索、检索和可视化。MDRepo 建立在开源 CyVerse 研究网络基础设施之上，能够存储 PB 级模拟，同时提供高带宽上传和下载功能，并为基于云的存储数据访问奠定基础。