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voelzlab.bsky.social
Professor of Chemistry at Temple University. Molecular simulation, stat mech, ML/DL, protein dynamics, biophysics, Bayesian inference, computational design, drug discovery. https://orcid.org/0000-0002-1054-2124 https://sites.temple.edu/voelzlab
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CALVADOS-RNA is now published doi.org/10.1021/acs.... This is a simple model for flexible RNA that complements and works with the CALVADOS protein model. Work led by Ikki Yasuda who visited us from Keio University. Try it yourself using our latest code for CALVADOS github.com/KULL-Centre/...

"… it is the words and actions of all members of the scientific community … that form the collective voice of science …," writes @holdenthorp.bsky.social in a new #ScienceEditorial. scim.ag/4hR6ux0

From my NIH SRO: MSFA postponed.

Just RSVP'ed for the @standupforscience.bsky.social rally in DC on March 7. See you there! standupforscience2025.org

www.nature.com/articles/d41...

RT please: Just 1.5 months away from our joint 3DBioinfo/3DSIG amazing conference! These are our two great keynote speakers! @rolanddunbrack.bsky.social & @silviaosuna.bsky.social! Check our preliminary programme here: www.iscb.org/3dbioinfo202... Registration link: www.iscb.org/3dbioinfo202...

Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence

I'm at @biophysicalsoc.bsky.social #BPS2025 with a bunch of folks from the Structural and Molecular Biophysics @flatironinstitute.org group-- come say hi and check out our posters/talks! @sonyahanson.bsky.social @pilarcossio.bsky.social @miroastore.bsky.social

#compchem Good read: Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias #compchemsky #biosky pubs.acs.org/doi/10.1021/...

The Lemkul Lab is heading to #BPS2025! We will have several posters and presentations, so please come chat with us about the latest in MD simulations of biomolecules, CADD, and the Drude polarizable force field! See you in LA! #compchemsky

Come meet our lab at #bps2025 in Los Angeles, starting this Saturday. We have 4 talks and 3 posters this year 🎉 More info 👇 @institutpasteur.bsky.social @cnrsbiologie.bsky.social

Three talks from my group on Sunday at #BPS2025 Cryptic pockets in crowded environments 9:30am in Rm 502A Allosteric glues inhibit G proteins noon in Rm 515B Antibody dynamics 5:30pm in Rm 502A

Incredible: Russ Vought’s daughter has cystic fibrosis and benefits from a “miracle drug” made possible by the National Institutes of Health—an agency Vought now aims to gut as part of the Project 2025 attack www.motherjones.com/politics/202... Scoop from @motherjones.com’s @metrauxjulia.bsky.social

First direct chemical synthesis of a gene over 1700 nucleotides long covered by @chemistryworld.com! Read the full paper in Chemical Science (which is free to read!) here: pubs.rsc.org/en/content/a... #ChemSky 🧪 #ChemBio

My editorial on the indirect cuts. This is an opportunity for campuses to come together to make the case for higher education. Leaders need to step up and ask for support and lead. www.science.org/doi/10.1126/...

“Our competitors are loving watching us do this …at the very time when we’re in a global competition that is determined by technological capability. This is certainly not the time when you want to be cutting down on the research acumen of the United States.” www.chronicle.com/article/rese...

This is what we did in 2017. Is it time for another March for Science? www.nytimes.com/2017/04/22/s...

Can’t believe I’m typing this but… FUCK IT IM PLANNING A STAND UP FOR SCIENCE PROTEST IN DC. If you want to be involved, be dm me. I’m nervous, I’ve never done this before, but we gotta be the change we want to see in the world.

The Howard Hughes Medical Institute, the nation’s largest private funder of biomedical research, yesterday killed a $60 million program aimed at making universities’ STEM education more inclusive. scim.ag/3EtS0US

arstechnica.com/science/2025...

A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it. www.science.org/content/blog...

Our paper is now out in @elife.bsky.social! We performed @cg-martini.bsky.social MD simulations to capture >700 lipid scrambling events in 27 TMEM16 structures to systematically study their lipid scrambling rates and mechanisms. 📃 doi.org/10.7554/eLife.105111.1

Thrilled to take a break from doom and gloom to share our latest work collaborating with the DeGrado lab! We took a de novo designed protein, screened it for ligand binding using X-rays, and used the hits to evolve two wildly different functions: fluorescent turn-on and Kemp elimination catalysis. 🧵

“If the freeze is not stopped, I might lose my house." Some NSF-funded postdocs are having trouble paying rent and credit card bills because their salaries were paused this week, even though the federal funding freeze memo was rescinded. www.statnews.com/2025/01/30/t...

Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X https://go.nature.com/42tH8Ai

Trump hits NIH with ‘devastating’ freezes on meetings, travel, communications, and hiring | Science | AAAS www.science.org/content/arti...

New preprint out from @voelzlab.bsky.social ! pylambdaopt is a method for optimizing an alchemical path from a single short trial. The method is based on equalizing the thermodynamic length between λ's and using the predicted mixing time of the transition matrix to optimize the number of λ's...🧵

We are happy to announce our Keynote Speakers! Drs. @rommieamaro.bsky.social & Dennis X. Hu (@drughunter.com) will be speaking at the 2025 Free Energy Workshop in Boston, MA, hosted at the Merck Research Laboratories. Submit an abstract by January 15th at: tinyurl.com/FEWorkshopAb...

Protein language models excel at generating functional yet remarkably diverse artificial sequences. They however fail to naturally sample rare datapoints, like very high activities. In our new preprint, we show that RL can solve this without the need for additional data: arxiv.org/abs/2412.12979

New version of Dockformer preprint landed on arXiv. This virtual screening docking method outperforms all Deep Learning-based approaches, achieving success rates of 90.53% on PDBbind and 82.71% on PoseBusters. Expected to accelerate drug discovery and reduce drug design costs.

Our new preprint describes an allosteric glue. Here, "glue" refers to a compound that causes two proteins to stick together. Usually the glue touches both proteins but here it only has to touch one! foldingathome.org/2024/12/18/a...

What to my wondering eyes should appear, but UCSF BMI student and Temple alum Rashad Reid visiting campus! #TempleMade @templechemistry.bsky.social @temple.edu

Congratulations to our Faculty and Staff who won CST awards today! Prof. Carol Manhart was named the Robert Smith Early Career Professor. Profs. Graham Dobereiner and Jonathan Smith won Dean's Distinguished Teaching Awards. And Tanya Santiago won the Ralph Jenkins Award for service to CST!!!

Great talk from first-year Bioinformatics PhD student Jason Cargill at the Temple BIO-BINF Rotation Talks!

1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations: bit.ly/plaid-proteins 🧵

Another deep-learning approach to sample conformational ensembles of proteins: BioEmu, out of Microsoft Research. www.biorxiv.org/content/10.1...

I'm thrilled to announce a new preprint describing collaborative work with Ajay Jain and Ann Cleves Jain, "Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows". arxiv.org/abs/2412.02889

Too many requests for money this Giving Tuesday? Consider giving your spare CPU/GPU cycles to advance biomedical research instead! Download our software and join our community of citizen scientists here: foldingathome.org/start-folding/

AF3 BEST METHOD followed by cluspro but also some conversion errors

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

New paper from the Voelz Lab!! (@voelzlab.bsky.social) Improved Estimates of Folding Stabilities and Kinetics with Multiensemble Markov Models Si Zhang, Yunhui Ge, and Vincent A. Voelz Biochemistry 2024 63 (22), 3045-3056

An update on our engineered PPI prediction challenge originally posted on the other platform... www.dickinsonlab.uchicago.edu/ppi-challenge We got many submissions. Interestingly, most approaches were able to get ~25% accurate (meaning the #1 predicted interaction was the real one) 1/n

My deep learning course at the University of Geneva is available on-line. 1000+ slides, ~20h of screen-casts. Full of examples in PyTorch. fleuret.org/dlc/ And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!) fleuret.org/lbdl/

I'm excited to share a new manuscript with Jiaqi Zhu characterizing the conformational ensembles of covalent adducts formed by a disordered protein and small molecule drugs: biorxiv.org/content/10.1... Code + Ensembles: github.com/paulrobustel...

Jumping on the word cloud trend. scholargoggler.com

If you want to help your students move from just writing code and scripts to actually developing scientific software that is useable and maintainable in the long-term, check out our latest paper in JCE. pubs.acs.org/doi/10.1021/...

I am excited to announce publication of our latest BindingDB update paper! academic.oup.com/nar/advance-... Please repost, as I am *just* getting started on BlueSky-- thanks!