Miranda-Quintana group

Best practices to cluster ultra-large molecular libraries: www.biorxiv.org/content/10.1...

YouTube video by Samuel Kim Music One Piece OST: Overtaken | EPIC VERSION (Drums of Liberation)

Soundtrack before the semester's last lecture:
www.youtube.com/watch?v=bfW6...

mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories We present mdBIRCH, an online clustering method that adapts the BIRCH CF-tree to molecular dynamics (MD) data by using a merge test calibrated directly to RMSD. Each arriving frame is routed to the ne...

Clustering MD simulations instantaneously with #mdBIRCH: www.biorxiv.org/content/10.1...

Typing this over smoke signals

Finally out: the most time- and memory-efficient way to cluster ultra-large molecular libraries!
Preprint: lnkd.in/emkeU_NH
Code: lnkd.in/euHc5s7U

1 BILLION molecules
1 workstation
2 hours
< 55 GB RAM
Check the code: github.com/mqcomplab/bb...

Productive Sunday

Unfolding the pins ;)

I still get some credit for setting up the initial conditions, right?

Thanks for the very kind words @aringermcdonald.bsky.social!!

🤣 Can I apply to be your postdoc?

We are looking for 2-3 prospective graduate students to join our group starting the Fall 2026 term. Main projects include method development for ML, MD, drug design, and QM.
Please, apply through: lnkd.in/gnM_wC_H

The Shape of Chemical Space The concept of chemical space is critical in cheminformatics, medicinal chemistry, and machine learning applications. Despite this, the high dimensionality of molecular representations greatly complic...

The shape of chemical space: www.biorxiv.org/content/10.1...
github.com/mqcomplab/NAMI

Time and memory benchmark of BitBIRCH vs clustering in nvMolKit
Code: github.com/mqcomplab/bb...

GitHub - mqcomplab/BitBIRCH_AC Contribute to mqcomplab/BitBIRCH_AC development by creating an account on GitHub.

The fastest way to identify or completely avoid activity cliffs: github.com/mqcomplab/Bi...

Thanks! Erik was working on some of the coolest applications of BitBIRCH. This new implementation is way more efficient than the previous one, so hopefully it'll be helpful.

All the best with the new nakamas!

GitHub - mqcomplab/bblean Contribute to mqcomplab/bblean development by creating an account on GitHub.

Clustering hundreds of millions of molecules in a single workstation is now a possibility!
Check the new code: github.com/mqcomplab/bb...

There are so many silly, obscure, Lord of the Rings references in my tenure talk that I might need to release a "behind the scenes/director's cut" going over them

What a crew! #OnePiece

Congrats!!

Preparing the slides for the departmental "tenure talk"

Lord of the Rings could meet a stretchy rubber pirate and a guy with a sword in his mouth and I'd still....oh wait.....

LOL I got a message with this from a certain secret common friend (@adrianroitberg.bsky.social). Looks very cool, but we know what's the superior story ;)

MDAnalysis User Group Meeting (logo)

Come to the @mdanalysis.bsky.social User Group Meeting at Arizona State University in November. See www.mdanalysis.org/2025/07/15/u... for our keynote speakers and more updates.

Great opportunity for junior researchers to present their work and to network with the MDAnalysis community.

The Klem Lab at LSU is hiring a postdoctoral researcher in computational biochemistry!
Application info: klem-research-group.github.io/join/
♻️ Please share with anyone who might be interested! #chemjobs #postdoc #compchem #biochemistry #enzymes

Has to be the whole population, of course!

LOL, not on Netflix, but I do replay the movies in my head constantly HAHA