A team of researchers from multiple institutions worked together to use U.S. National Science Foundation (NSF) ACCESS allocations on Jetstream2 at Indiana University to create the first open-access repository designed to house and analyze hundreds of thousands of community-contributed molecular dynamics simulations – potentially revolutionizing how scientists understand protein structures and drug interactions.
“Molecular dynamics simulations provide crucial insights into how biomolecules change shape and interact with other molecules,” said Amitava Roy, first author and affiliate professor with the Department of Biomedical and Pharmaceutical Sciences at the University of Montana. “These simulations represent a largely untapped resource for training machine learning models that will transform predictions of structure, dynamics and drug interactions.”
Travis Hughes, co-author and associate professor of biochemistry at the University of Montana, explained that the new platform, called MDRepo, addresses a critical gap in scientific infrastructure by providing standardized storage and access to valuable simulation data that was previously scattered across individual computers worldwide.
The work has been detailed in a recent issue of the Nucleic Acids Research Journal.
“MDRepo offers a robust infrastructure with a straightforward process for contributing and accessing simulations,” said Travis Wheeler, lead author and associate professor of pharmacy at the University of Arizona. “Creating this system would not have been possible without ACCESS allocations on the powerful Jetstream2 supercomputer.”
Creating this system would not have been possible without ACCESS allocations on the powerful Jetstream2 supercomputer.
–Travis Wheeler, associate professor of pharmacy, University of Arizona
Wheeler said that MDRepo enables scientists to search, retrieve, analyze and visualize data contributed by researchers globally. Built on the open-source CyVerse research cyber-infrastructure, MDRepo can store petabytes of simulations while providing high-bandwidth upload and download capabilities. The platform also supports common downstream analyses and lays groundwork for future cloud-based access and training of the next generation of AI tools for drug discovery.
The authors have also published an opinion piece in Nature that further discusses the importance of shared data via repositories like MDRepo.
Resource Provider Institution(s): Indiana University (IU)
Resources Used: Jetstream2
Affiliations: University of Montana, University of Arizona
Funding Agency: The work was funded by NSF (DBI grant nos. 0735191, 1265383 and 1743442) along with support from the University of Arizona Research, Innovation & Impact through BIO5 and IT4IR TRIF funds. Allocations on Jetstream2 were provided by the NSF ACCESS program (allocation no. BIO230080).
Grant or Allocation Number(s): 0735191, 1265383, 1743442, BIO230080
The science story featured here was enabled by the U.S. National Science Foundation’s ACCESS program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.