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: 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...

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

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

Preparing the slides for the departmental "tenure talk"

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

The time evolution of chemical space: pubs.acs.org/doi/full/10....

How to treat yourself after a tenure tour... @adrianroitberg.bsky.social, @olexandr.bsky.social, wanna drop by? 🤣

Thanks to #pandaexpress for the support before submitting my tenure packet.

Gibbs, Onsager, and Kirkwood. Boltzmann's tombstone will forever be the best one, but Onsager's is pretty epic!

A truly epic visit, great science talks, making new friends, and getting to eat some of the best ice cream ever thanks to @ltchong.bsky.social and @olexandr.bsky.social. Pittsburgh was absolutely legendary! Oh, and of course I went to pay my respects to Pople!

Two assistant professors in their tenure tours. The guy in white looks way more lively.

Very happy to announce that we received an #NSFCAREER award that'll help us develop new ab initio methods to tackle complex electronic structure problems.

@lexinc.bsky.social with the stellar dissertation defense on unsupervised #ML techniques for #MD simulations 🎉

You cannot walk into Mordor with #BitBIRCH, but you can cluster billions of molecules: github.com/mqcomplab/bi...

Little-known fact, the "B" in BIRCH stands for "B"owling

#BitBIRCH just got better! Thanks to Kenneth López-Pérez, Kate Huddleston, and Vic Jung for the stellar effort! If you want to know more about it, drop by Hall B-1, Room 4, this Tuesday, 3/25 #ACSSpring2025 Preprint: lnkd.in/dTymmFi7 Code: lnkd.in/ewA4d-jb

Great to meet up with Lexin and Ramon from @groupquintana.bsky.social today at #ACSSpring2025. Great work coming from their group and we are excited to work with them!

Providing more insights on how charge transfer can dictate the behavior of catalysts, through a new look on the Sabatier Principle: lnkd.in/eETYAR37. As always, a great collaboration with Jens Smiatek and his team!

A summary of our group's presence at #ACSSpring25: Sunday, 10:15, @lexinc.bsky.social will talk about #MDANCE (Room 29A) Tuesday, 11:30, come for the latest in #BitBIRCH (Hall B-1, Room 4) Tuesday, 2:00, we'll talk about our work on charge transfer (Hall F, Room 2)

Today's featured article introduces BitBIRCH by López Pérez, Jung, Miranda-Quintana et al. BitBIRCH uses a tree structure similar to the BIRCH algorithm to provide molecular library clustering in O(N) time. Read the #openaccess article here: doi.org/10.1039/D5DD...

LOL thanks a lot!

Well, the tenure tour theme song is out: www.youtube.com/watch?v=KmMl...

Starting a long West Coast trip at @ucirvine.bsky.social, then I'll be at @ucsandiego.bsky.social since 3/19, then staying in town for #ACSSpring25. Reach out if you want to talk about the latest on #BitBIRCH (lnkd.in/eDMGCjCB), #iSIM (lnkd.in/e3rDbQdC) and #MDANCE (lnkd.in/eWHcFpJZ).

#BitBIRCH out @digital-discovery.rsc.org: pubs.rsc.org/en/content/a...

Getting the office ready for a semester full of travels

n-ary guided density clustering with a musical acronym: CADENCE (www.biorxiv.org/content/10.1...), courtesy of @lexinc.bsky.social. The latest update to MDANCE: github.com/mqcomplab/MD...

Is chemical space really expanding? Check Kenneth's pipeline for studying the evolution of chemical diversity over time, together with Eloy Felix and Jose Luis Medina Franco and his team: www.biorxiv.org/content/10.1...

Is Tanimoto a metric? Not really, but check this last manuscript on how to turn it into one: www.biorxiv.org/content/10.1...

After 5 years at UFChemistry is time to go on the "tenure tour". But, is it really a tour without music? So...stay tuned, the MQ-Lab will be releasing its first rap track this month ;)

Great collaboration with @ltchong.bsky.social on pathway ensemble clustering. 🌟SHINE🌟 is out in @biorxiv-biophys.bsky.social : www.biorxiv.org/content/10.1..., and of course @lexinc.bsky.social got it in #MDANCE as well: github.com/mqcomplab/MD...

Feeling quite stupid now: GOLD roger SILVERs Rayleigh sCOPPER gabban #OnePiece

Thanks to Kate Huddleston and Kenneth López-Pérez, now you can also use BitBIRCH (www.biorxiv.org/content/10.1...) with other similarity indices, like Sokal-Michener and Russel-Rao. Check their latest implementation: github.com/mqcomplab/bi... #clustering #drugdesign

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

Tired of how slow hierarchical clustering is? Tired of finding optimum k values for k-means? We present eQual to you: biorxiv.org/content/10.1... the last member of the #MDANCE family, it bridges the gap between k-means and HAC. Thanks to @lexinc.bsky.social and @daniel-r-roe.bsky.social!

From today's exam! @adrianroitberg.bsky.social, I have it in my office ;)

import numpy as plt

iSIM can give you the mean of all the pairwise similarities in a set in O(N), but now we've shown that it can also give you the standard deviation of the similarities in O(N) as well! Check Kenneth's last preprint on iSIM-sigma: www.biorxiv.org/content/10.1...

Attention #LatinXChemists (those in go.bsky.app/Dk2yzWa and not), this is a great opportunity to show up your work!

Following on the steps of @wpwalters.bsky.social, Kate Huddleston added a BitBIRCH (www.biorxiv.org/content/10.1...) analysis to the data splitting notebook (github.com/mqcomplab/bi...)

About activity cliffs, sampling, similarity, and ML training: onlinelibrary.wiley.com/doi/10.1002/...

At this point might as well fully commit to the #TolkienTuesday meme and celebrate Elrond's grandfather in the thermodynamics class

There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... .

@miarosenfeld.bsky.social @drklemistry.bsky.social , there's no ACS COMP page here?