MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins
Amitava Roy, Ethan Ward, Illyoung Choi, Michele Cosi, Tony Edgin, Tudor Hughes, Md Nazrul Islam, Asif M. Khan, Aakash Kolekar, Mariah Rayl, Isaac Robinson, Paul Sarando, Edwin Skidmore, Tyson L. Swetnam, Mariah Wall, Zhuoyun Xu, Michelle Lynn Yung, Nirav Merchant, Travis J. Wheeler
Abstract
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.