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👇

Achira Building foundation simulation models for drug discovery

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

Yes, that's the part I find interesting now. In my head I draw a vague line between struc bio (data) and computational biophysics (physics) though, and I think the struc bio side has more to offer than it is currently.

My head says you are right, my heart says you are wrong.

I feel like with the coverage of data now available to us there must be some principles we have yet to find.

Yes, that fits with the idea of proteins that don't carry out a function until they have to compensate for the lack of another protein. They had the property all along.

Figure 1 from the preprint

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

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...

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...

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...

Thank you for being annoying OR: whack 'em if you got 'em

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-...

Looks like the original post was deleted, here is the updated one.

This is a great conference for both free energy methods and force field development.

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.

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 ...

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.

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

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

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...

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

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

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...

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.

If you know, you know.

YouTube video by Mind Unlocked Dr Joe Greener: a Career in Research, Application Advice, Open Source | LMB Computational Biologist

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...

🚨 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...

📢 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...

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 ...

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...

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.

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...

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...

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.

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.

Screenshot of a PyMOL window showing a simulation of water with oxygen atoms clustered.

Round 1 of our machine learning potential really wants oxygen atoms in water to cluster together 😂

GitHub - BioJulia/BioStructures.jl: A Julia package to read, write and manipulate macromolecular structures A Julia package to read, write and manipulate macromolecular structures - BioJulia/BioStructures.jl

New release of BioStructures.jl just out: github.com/BioJulia/Bio....

Featuring chi angle calculation, mmCIF secondary structure reading and bonded graph construction all thanks to Tim Holy.

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.