Joe Greener
jgreener64.bsky.social
Joe Greener
@jgreener64.bsky.social
Computational chemist/structural bioinformatician working on improving molecular simulation at MRC Laboratory of Molecular Biology. jgreener64.github.io
Pinned
I wrote a blog post about the future of structural bioinformatics.

Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?

Let me know what you think.

jgreener64.github.io/posts/struct...
Where next for structural bioinformatics?
jgreener64.github.io
Finally got round to reading this great review on dispersion interactions from 2012. These interactions are crucial for biomolecular systems.

pubs.aip.org/aip/jcp/arti...
pubs.aip.org
November 11, 2025 at 12:31 PM
The latest release of Molly has Ewald/PME methods, constraint support on GPU, better virial support, new couplers and more.

Do try it out if you like flexible molecular simulations. More features and performance coming soon.

github.com/JuliaMolSim/...
GitHub - JuliaMolSim/Molly.jl: Molecular simulation in Julia
Molecular simulation in Julia. Contribute to JuliaMolSim/Molly.jl development by creating an account on GitHub.
github.com
November 3, 2025 at 5:48 PM
Reposted by Joe Greener
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
Reposted by Joe Greener
Achira is growing! We’re looking for talented software engineers, ML research engineers, and AI/ML scientists to join our team in building foundation simulation models to power the future of drug discovery.

Apply at achira.ai
Achira
Building foundation simulation models for drug discovery
achira.ai
October 24, 2025 at 12:20 PM
Reposted by Joe Greener
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️

www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
I wrote a blog post about the future of structural bioinformatics.

Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?

Let me know what you think.

jgreener64.github.io/posts/struct...
Where next for structural bioinformatics?
jgreener64.github.io
October 15, 2025 at 2:16 PM
A shame that GigaScience's Hong Kong team have been laid off by the owners, BGI. GigaScience has been influential in its push for open data.

www.open-bio.org/2025/09/30/2...
GigaScience: 15 years of great open science publishing & the end of an era?
To begin something is difficult; to keep something going is a different challenge. Even when it is the right thing to do, if it does not yield economic benefit in the short term, it may be difficult t...
www.open-bio.org
October 1, 2025 at 10:51 AM
Another great blog post by @mastroianni.bsky.social, this time explaining why being a scientist can sometimes feel so... annoying?

www.experimental-history.com/p/thank-you-...
Thank you for being annoying
OR: whack 'em if you got 'em
www.experimental-history.com
September 30, 2025 at 3:14 PM
This is a great conference for both free energy methods and force field development.
September 23, 2025 at 4:43 PM
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.
September 19, 2025 at 12:32 PM
Reposted by Joe Greener
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
July 16, 2025 at 3:13 AM
Reposted by Joe Greener
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
July 7, 2025 at 8:21 AM
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
July 4, 2025 at 4:11 PM
Reposted by Joe Greener
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
June 25, 2025 at 1:49 PM
Reposted by Joe Greener
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
June 20, 2025 at 3:53 PM
Interested in a postdoc position combining computational protein design and molecular simulation? There is an open position in my group at the MRC-LMB in Cambridge, UK.

www.nature.com/naturecareer...

Feel free to message me with any questions.
Postdoctoral Scientist - Structural Studies - Dr Joe Greener - LMB 2633 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840475
Postdoctoral Scientist Salary £41,344 per annum  Fixed Term – 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postd...
www.nature.com
June 16, 2025 at 10:47 AM
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
June 13, 2025 at 5:50 PM
Reposted by Joe Greener
🚨 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
June 13, 2025 at 11:12 AM
Reposted by Joe Greener
📢 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...
June 3, 2025 at 2:47 PM
Reposted by Joe Greener
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
May 31, 2025 at 6:06 PM
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.
May 28, 2025 at 4:10 PM
Reposted by Joe Greener
The amazing Sofia Lövestam initiated the below project, when she became interested in the vault particles that we sometimes observe in #cryoEM images of brain-derived #amyloid filaments.
www.biorxiv.org/content/10.1...
Cryo-EM structure of the vault from human brain reveals symmetry mismatch at its caps
The vault protein is expressed in most eukaryotic cells, where it is assembled on polyribosomes into large hollow barrel-shaped complexes. Despite its widespread and abundant presence in cells, the bi...
www.biorxiv.org
May 28, 2025 at 7:33 AM
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.
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
May 19, 2025 at 6:10 PM
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.
May 16, 2025 at 10:42 AM
Round 1 of our machine learning potential really wants oxygen atoms in water to cluster together 😂
May 14, 2025 at 12:42 PM