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Miranda-Quintana group

@groupquintana.bsky.social
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RamO(N) Miranda Quintana Theoretical and Computational chemistry quintana.chem.ufl.edu #chemsky #compchemsky

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Miranda-Quintana group @groupquintana.bsky.social · 05/05/2026
#postdoc position in our lab explore.jobs.ufl.edu/en-us/job/53...
explore.jobs.ufl.edu
University of Florida - Details - Chemistry Post-Doctoral Associate - Unsupervised and Generative Machine Learning
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Miranda-Quintana group @groupquintana.bsky.social · 09/04/2026
Beware of negative electron densities lnkd.in/e6iEXjjX
lnkd.in
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Miranda-Quintana group @groupquintana.bsky.social · 09/04/2026
Nothing like #iChem to process ultra-large chemical libraries! github.com/mqcomplab/iC...
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Miranda-Quintana group @groupquintana.bsky.social · 10/03/2026
Excited to be at my first CUP (in lovely Santa Fe), happy to talk about billions, trillions,......, and more molecules ;)
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Miranda-Quintana group @groupquintana.bsky.social · 02/12/2025
Best practices to cluster ultra-large molecular libraries: www.biorxiv.org/content/10.1...
biorxiv.org
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Miranda-Quintana group @groupquintana.bsky.social · 20/11/2025
Soundtrack before the semester's last lecture: www.youtube.com/watch?v=bfW6...
youtube.com
One Piece OST: Overtaken | EPIC VERSION (Drums of Liberation)
YouTube video by Samuel Kim Music
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Miranda-Quintana group @groupquintana.bsky.social · 07/11/2025
Clustering MD simulations instantaneously with #mdBIRCH: www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Miranda-Quintana group @groupquintana.bsky.social · 24/10/2025
Finally out: the most time- and memory-efficient way to cluster ultra-large molecular libraries! Preprint: lnkd.in/emkeU_NH Code: lnkd.in/euHc5s7U
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Miranda-Quintana group @groupquintana.bsky.social · 19/10/2025
1 BILLION molecules 1 workstation 2 hours < 55 GB RAM Check the code: github.com/mqcomplab/bb...
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Miranda-Quintana group @groupquintana.bsky.social · 05/10/2025
Productive Sunday
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Miranda-Quintana group @groupquintana.bsky.social · 04/10/2025
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Miranda-Quintana group @groupquintana.bsky.social · 29/09/2025
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
lnkd.in
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Miranda-Quintana group @groupquintana.bsky.social · 26/09/2025
The shape of chemical space: www.biorxiv.org/content/10.1... github.com/mqcomplab/NAMI
biorxiv.org
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...
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Miranda-Quintana group @groupquintana.bsky.social · 26/09/2025
Time and memory benchmark of BitBIRCH vs clustering in nvMolKit Code: github.com/mqcomplab/bb...
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Miranda-Quintana group @groupquintana.bsky.social · 17/09/2025
The fastest way to identify or completely avoid activity cliffs: github.com/mqcomplab/Bi...
github.com
GitHub - mqcomplab/BitBIRCH_AC
Contribute to mqcomplab/BitBIRCH_AC development by creating an account on GitHub.
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Miranda-Quintana group @groupquintana.bsky.social · 16/09/2025
Clustering hundreds of millions of molecules in a single workstation is now a possibility! Check the new code: github.com/mqcomplab/bb...
github.com
GitHub - mqcomplab/bblean
Contribute to mqcomplab/bblean development by creating an account on GitHub.
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Miranda-Quintana group @groupquintana.bsky.social · 02/09/2025
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
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Miranda-Quintana group @groupquintana.bsky.social · 28/08/2025
What a crew! #OnePiece
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Miranda-Quintana group @groupquintana.bsky.social · 21/08/2025
Preparing the slides for the departmental "tenure talk"
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Oliver Beckstein [he/him] @orbeckst.bsky.social · 16/07/2025
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.
MDAnalysis User Group Meeting (logo)
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Heidi Klem @drklemistry.bsky.social · 02/07/2025
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
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Miranda-Quintana group @groupquintana.bsky.social · 14/06/2025
The time evolution of chemical space: pubs.acs.org/doi/full/10....
pubs.acs.org
Growth vs Diversity: A Time-Evolution Analysis of the Chemical Space
It is well-known that the number of compounds (both synthesized and theoretical ones) is rapidly increasing. Hence, it would be obvious to affirm that the chemical space is expanding. However, is the ...
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Miranda-Quintana group @groupquintana.bsky.social · 25/05/2025
How to treat yourself after a tenure tour... @adrianroitberg.bsky.social, @olexandr.bsky.social, wanna drop by? 🤣
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Miranda-Quintana group @groupquintana.bsky.social · 23/04/2025
Thanks to #pandaexpress for the support before submitting my tenure packet.
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Miranda-Quintana group @groupquintana.bsky.social · 23/04/2025
Gibbs, Onsager, and Kirkwood. Boltzmann's tombstone will forever be the best one, but Onsager's is pretty epic!
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Miranda-Quintana group @groupquintana.bsky.social · 19/04/2025
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!
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Miranda-Quintana group @groupquintana.bsky.social · 19/04/2025
Two assistant professors in their tenure tours. The guy in white looks way more lively.
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Miranda-Quintana group @groupquintana.bsky.social · 15/04/2025
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.
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Miranda-Quintana group @groupquintana.bsky.social · 15/04/2025
@lexinc.bsky.social with the stellar dissertation defense on unsupervised #ML techniques for #MD simulations 🎉
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Miranda-Quintana group @groupquintana.bsky.social · 08/04/2025
You cannot walk into Mordor with #BitBIRCH, but you can cluster billions of molecules: github.com/mqcomplab/bi...
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Miranda-Quintana group @groupquintana.bsky.social · 29/03/2025
Little-known fact, the "B" in BIRCH stands for "B"owling
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Miranda-Quintana group @groupquintana.bsky.social · 25/03/2025
#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
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Justin Lemkul @justinlemkulvt.bsky.social · 24/03/2025
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!
Lemkul and Miranda Quintana group members at lunch. From left, Haley Michel, Lexin Chen, Laura Gil Pineda, Esmat Mohammadi, Ramon Miranda Quintana, and Justin Lemkul.
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Miranda-Quintana group @groupquintana.bsky.social · 22/03/2025
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!
lnkd.in
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Miranda-Quintana group @groupquintana.bsky.social · 21/03/2025
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)
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Digital Discovery @digital-discovery.rsc.org · 19/03/2025
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...
An icon for bit birch, surrounded by molecule structures, in a computer window.
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Miranda-Quintana group @groupquintana.bsky.social · 19/03/2025
LOL thanks a lot!
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Miranda-Quintana group @groupquintana.bsky.social · 18/03/2025
Well, the tenure tour theme song is out: www.youtube.com/watch?v=KmMl...
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Miranda-Quintana group @groupquintana.bsky.social · 17/03/2025
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).
lnkd.in
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Miranda-Quintana group @groupquintana.bsky.social · 13/03/2025
#BitBIRCH out @digital-discovery.rsc.org: pubs.rsc.org/en/content/a...
pubs.rsc.org
BitBIRCH: Efficient clustering of large molecular libraries
The widespread use of Machine Learning (ML) techniques in chemical applications has come with the pressing need to analyze extremely large molecular libraries. In particular, clustering remains one of...
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Miranda-Quintana group @groupquintana.bsky.social · 01/03/2025
Getting the office ready for a semester full of travels
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Miranda-Quintana group @groupquintana.bsky.social · 01/03/2025
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...
biorxiv.org
CADENCE: Clustering Algorithm - Density-based Exploration and Novelty Clustering with Efficiency
Unsupervised learning techniques play a pivotal role in unraveling protein folding landscapes, constructing Markov State Models, expediting replica exchange simulations, and discerning drug binding pa...
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Miranda-Quintana group @groupquintana.bsky.social · 24/02/2025
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...
biorxiv.org
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Miranda-Quintana group @groupquintana.bsky.social · 23/02/2025
Is Tanimoto a metric? Not really, but check this last manuscript on how to turn it into one: www.biorxiv.org/content/10.1...
biorxiv.org
Is Tanimoto a metric?
No. However, here we show how to generate a metric consistent with the Tanimoto similarity. We also explore new properties of this index, and how it relates to other popular alternatives. ### Competi...
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Miranda-Quintana group @groupquintana.bsky.social · 16/02/2025
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 ;)
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Miranda-Quintana group @groupquintana.bsky.social · 10/02/2025
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...
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Miranda-Quintana group @groupquintana.bsky.social · 07/02/2025
Feeling quite stupid now: GOLD roger SILVERs Rayleigh sCOPPER gabban #OnePiece
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Miranda-Quintana group @groupquintana.bsky.social · 03/02/2025
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
biorxiv.org
Efficient clustering of large molecular libraries
The widespread use of Machine Learning (ML) techniques in chemical applications has come with the pressing need to analyze extremely large molecular libraries. In particular, clustering remains one of...
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Reposted by Miranda-Quintana group
Frank Noe @franknoe.bsky.social · 06/12/2024
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...
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Miranda-Quintana group @groupquintana.bsky.social · 05/12/2024
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!
biorxiv.org
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