MDRepo is has exceeded 500K individual open access #MolecularDynamics trajectories and is rapidly approaching 80,000 entries. We've received submissions containing ~20k entries and others with just a few - all contributions are welcome!

PLAS-20k (www.nature.com/articles/s41597-023-02872-y) introduced nearly 100,000 simulatons over close to 20,000 protein-ligand systems, intended for training AI binding inference models. We've worked with the PLAS-20k creators to make them available in mdrepo.org.

We agree with all of our heart

Neil Hall@neilhall.bsky.social · last mo.

Biological Databases are critical infrastructure - not projects. As so much effort is put into harnessing AI to solve all our problems, we are allowing the foundational data resources crumble. Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...

mdrepo.org now has its own account (that's me!) Follow the account for updates on content and functionality.

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 2mo ago

@wheelerlab.org is talking about his effort to build a resource for protein dynamics (PDB for MD). MDRepo is a repository to store simulation data. This is really needed to push the needle in design, function and more. Please help make it successful by sharing your MD data. #ismb2026 🌐 mdrepo.org

Dynamic PDB (arxiv.org/abs/2408.12413) ran 1-µs all-atom MD on ~12,600 PDB structures, and has released ~3,300 so far, downsampled to 1 ns frame spacing. Those are now available in mdrepo.org. We'll expand coverage as the remainder are released, with links out to the full-resolution trajectories.

mdrepo.org is also designed to support user-contributed data. We currently host a few thousand user-contributed entries, with a lot more in flight. Add yours to the growing list, so others can see and use your data! mdrepo.org/faq

MDRepo@mdrepo.bsky.social · last mo.

Status update for mdrepo.org We've ingested the mdCATH dataset: 26,990 replicate sets (5,398 CATH domains, each at 5 temps). A couple examples: mdrepo.org/explore/MDR0... mdrepo.org/explore/MDR0... We now provide easy access to data from mdCATH, MISATO, ATLAS, and GPCRmd; more coming soon.

Status update for mdrepo.org We've ingested the mdCATH dataset: 26,990 replicate sets (5,398 CATH domains, each at 5 temps). A couple examples: mdrepo.org/explore/MDR0... mdrepo.org/explore/MDR0... We now provide easy access to data from mdCATH, MISATO, ATLAS, and GPCRmd; more coming soon.

It's the moment the whole world has been waiting for! the MDRepo bluesky account is here. We'll give occasional updates about the status of MDRepo - what notable new data have made their way into the system, what new features are available, etc. For starters: we now have >50,000 replicate sets