Joe Greener
@jgreener64.bsky.social
530 followers 420 following 140 posts
Computational chemist/structural bioinformatician working on improving molecular simulation at MRC Laboratory of Molecular Biology. jgreener64.github.io
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jgreener64.bsky.social
The reversible molecular simulation paper is out in final form: www.pnas.org/doi/10.1073/....

Now including an example of fine-tuning MACE-OFF23 to fit the RDF of water. Thanks to the reviewers for useful comments.
jgreener64.bsky.social
Looks like the original post was deleted, here is the updated one.
feworkshop.bsky.social
Save the date, my fellow computational alchemists! The upcoming '26 Workshop on Free Energy Methods in Drug Design will be held in Barcelona, Spain, on May 4-6, 2026. The registration link will be sent soon!
jgreener64.bsky.social
This is a great conference for both free energy methods and force field development.
jgreener64.bsky.social
Interesting points about interdisciplinary research.

Having people in the same space talking over a long period of time (months) is one way to address this. It tends to happen organically, though, and is hard to plan.
Reposted by Joe Greener
carlbergstrom.com
1. Kevin Gross and I just posted a new science-of-science preprint.

This one explores the looming peer review crisis. As many of you know, it's becoming significantly more difficult for journal editors to find scholars willing to serve as peer reviewers for submitted manuscripts.
Will anyone review this paper? Screening, sorting, and the feedback cycles that imperil peer review
Scholarly publishing relies on peer review to identify the best science. Yet finding willing and qualified reviewers to evaluate manuscripts has become an increasingly challenging task, possibly even ...
arxiv.org
Reposted by Joe Greener
martinsteinegger.bsky.social
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
jgreener64.bsky.social
A real shame that the future of CASP is in doubt. There is still a lot of progress to be assessed (complexes, nucleic acids, ligands, ensembles). CASP has also been a pioneer in how to run blind assessments.

www.science.org/content/arti...
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
www.science.org
Reposted by Joe Greener
mrclmb.bsky.social
Excellent opportunity for a postdoc to join @jgreener64.bsky.social’s group at the LMB.
You’ll help develop novel molecular simulation methods to optimise sequences for diverse design tasks in computational protein design.
See: www.nature.com/naturecareer...
Apply by 13 JUL
#PostdocJobs #ScienceJobs
Joe Greener
Reposted by Joe Greener
labcosmo.bsky.social
Very proud to send Filippo Bigi to Vancouver to give an oral presentation at @icmlconf.bsky.social about our investigation of the use of "dark-side forces" in atomistic simulations. The final version is here openreview.net/forum?id=OEl... and it's worth a read even if you already read the #preprint
The dark side of the forces: assessing non-conservative force...
The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, have revolutionized the fields of computational chemistry and...
openreview.net
jgreener64.bsky.social
If you know, you know.
jgreener64.bsky.social
Yuchi Guo, a former Masters project student of mine, interviewed me for a new podcast. We talked about science, open source software and what makes a good life.

YouTube: www.youtube.com/watch?v=NZlE...
Apple: podcasts.apple.com/us/podcast/m...
Spotify: open.spotify.com/episode/1suM...
Dr Joe Greener: a Career in Research, Application Advice, Open Source | LMB Computational Biologist
YouTube video by Mind Unlocked
www.youtube.com
Reposted by Joe Greener
diegozea.bsky.social
🚨 We're hiring a Bioinformatics Engineer!
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...
Portail Emploi CNRS - Offre d'emploi - Ingénieur bioinformaticien – Analyse computationnelle des protéines intrinsèquement désordonnées (H/F)
emploi.cnrs.fr
Reposted by Joe Greener
colegroupncl.bsky.social
📢 New preprint: "A graph neural network charge model targeting accurate electrostatic properties of organic molecules" by @charlie-adams.bsky.social et al out now on @chemrxiv.bsky.social #compchem

doi.org/10.26434/che...
Reposted by Joe Greener
philipcball.bsky.social
It's an interesting phenomenon that some of the deepest questions about how life works have become what looks like impossibly obscure molecular biology stuck right at the back of Nature, which will never get covered by the science media. Like this. /1
www.nature.com/articles/s41...
DNA-guided transcription factor interactions extend human gene regulatory code - Nature
A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by ...
www.nature.com
jgreener64.bsky.social
The reversible molecular simulation paper is out in final form: www.pnas.org/doi/10.1073/....

Now including an example of fine-tuning MACE-OFF23 to fit the RDF of water. Thanks to the reviewers for useful comments.
jgreener64.bsky.social
Glad to see the MACE-OFF paper out in final form. They show that MLIPs can be relevant to biomolecules, I'm sure there will be lots more work in this area in the coming years.
colegroupncl.bsky.social
Now out in @jacs.acspublications.org ! 🎉 : "MACE-OFF: Short-Range Transferable Machine Learning Force Fields for Organic Molecules" by Dávid Kovács, @jhmchem.bsky.social, & team:
pubs.acs.org/doi/10.1021/...
MACE-OFF: Short-Range Transferable Machine Learning Force Fields for Organic Molecules
Classical empirical force fields have dominated biomolecular simulations for over 50 years. Although widely used in drug discovery, crystal structure prediction, and biomolecular dynamics, they generally lack the accuracy and transferability required for first-principles predictive modeling. In this paper, we introduce MACE-OFF, a series of short-range transferable force fields for organic molecules created using state-of-the-art machine learning technology and first-principles reference data computed with a high level of quantum mechanical theory. MACE-OFF demonstrates the remarkable capabilities of short-range models by accurately predicting a wide variety of gas- and condensed-phase properties of molecular systems. It produces accurate, easy-to-converge dihedral torsion scans of unseen molecules as well as reliable descriptions of molecular crystals and liquids, including quantum nuclear effects. We further demonstrate the capabilities of MACE-OFF by determining free energy surfaces in explicit solvent as well as the folding dynamics of peptides and nanosecond simulations of a fully solvated protein. These developments enable first-principles simulations of molecular systems for the broader chemistry community at high accuracy and relatively low computational cost.
pubs.acs.org
jgreener64.bsky.social
Benchmarking of an open, generic protocol shows decent performance for relative binding free energy calculations.

These methods are gradually making MD an important part of the drug discovery pipeline.
openfree.energy
If you weren't at @feworkshop.bsky.social in Boston last week, you missed Hannah Baumann giving the first sneak peek at results from our partner benchmarking study! Fortunately for you, Josh Horton wrote up a blog post about the early results: blog.omsf.io/the-free-ene...

#compChem
The Free Energy of Everything: Benchmarking OpenFE
Written by: Josh Horton, PhD Who is OpenFE and what do they do? Open Free Energy (OpenFE) sits at the nexus of academia and industry. We are developing an open-source software ecosystem for alchem...
blog.omsf.io
jgreener64.bsky.social
Round 1 of our machine learning potential really wants oxygen atoms in water to cluster together 😂
Screenshot of a PyMOL window showing a simulation of water with oxygen atoms clustered.
jgreener64.bsky.social
Had a great time at the @feworkshop.bsky.social and @omsf.io conferences. The future of open molecular software and free energy methods is looking good.

If anyone has any recommendations for Boston, MA for tomorrow then do let me know.
jgreener64.bsky.social
I just used the PyMod PyMOL plugin for the first time and am very impressed. It installed without a problem and let me model missing loops easily.
jgreener64.bsky.social
Had a great time at the Museu de les Ciències Príncipe Felipe in Valencia, Spain.

Saw lots of kids engaged with science and the Chromosome Forest exhibition covering much of biology. I can just about forgive the artistic licence in the DNA model.
Artistic model of DNA structure at the Museu de les Ciències Príncipe Felipe in Valencia, Spain.