Summary and outcomes from the “Structural databases in the exascale era” meeting

The Structural databases in the exascale era meeting, held on April 1, 2025, at Lady Margaret Hall, Oxford, brought together 13 members of the MDDB consortium and 15 external experts to advance the integration of molecular dynamics (MD) simulation data with established biological data repositories such as PDB and UniProt. The meeting featured presentations from different MD databases, discussions on annotation strategies, and exploration of tools to support analysis and interoperability, emphasising user accessibility for both expert and non-expert communities.

The group identified several key areas of progress, including the need for simplified, standardised vocabularies and metadata for annotations, such as those related to cryptic pockets, membrane properties, and the presence of small molecules. It was agreed that containerised workflows, particularly through tools like Docker, would be crucial for scalable analysis. Strategies for comparing simulations across different datasets, linking them to original publications, and enhancing data integration through robust APIs were also discussed. A shared document was established to collaboratively define and prioritise biologically meaningful annotations. The meeting also highlighted the importance of user-friendly interfaces and accessibility, with PDBe-KB’s approach to aggregated visualisation and simplified search functionalities serving as an inspiration for similar strategies within MDDB. Additionally, MDPosit was proposed as a central interface where users can search and access simulations across multiple databases. Ongoing development of the MDPosit API aims to improving metadata management, data grouping, and facilitating DOI assignments for better dataset citation. As a result, two working groups, a scientific and a technical one, were initiated to carry this momentum forward.