Joe Greener

The one science reform we can all agree on, but we're too cowardly to do OR: the long overdue forest fire

Catch the tiger!

www.experimental-history.com/p/the-one-sc...

Fun visit to @bindresearch.org today. They have some great ideas to find drugs that target disordered proteins and to make lots of IDP-ligand data available.

The screenshot of the release notes reads: A new version of TeX Live Utility is available! TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now? Release Notes: Changes Since 1.54 • Fix bug 137, homepage link in Help Book. • First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software. • Updated mirror list, which was three years out of date. • Added missing legacy mirrors, which was even more out of date. • Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database. Thanks for nothing, guys. Bug 142 and 144. • Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models. • Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.

There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.

The Indian plate is part of the Indo-Australian plate, which underlies the Indian Ocean and Bay of Bengal, and is moving north-east at an average of 60 mm/a (0.075 in/Ms).

I can overlook millimetres per year, but what utter anarchy of a unit is inches per megasecond

Kelly Nguyen announced as Laureate in Life Sciences at the 2026 Blavatnik Awards in the UK.

Congratulations to @kellythd-nguyen.bsky.social, Group Leader in the LMB’s Structural Studies Division, who has been named the Life Sciences Laureate at the 2026 Blavatnik Awards in the UK 🎉

Read the full news story here: mrclmb.ac.uk/news-events/...

#LMBNews #Blavatnik2026

A great position in our division is now open, do feel free to contact me with questions.

A useful initiative, as I've noticed that a lot of people use scientific software without citing it.

Don't even get me started on using large language models to run molecular dynamics. (4/4)

One use case for long time steps is to generate plausible pathway conformations for a slow conformational change, e.g. for protein fold switchers.

That seems a way away though, due to the Catch-22 of needing training data for conformations you want to see. (3/4)

In this context it makes more sense to train models to generate conformations from the underlying distribution (though I'm not yet convinced by models that do this).

As the time step gets longer you would increasingly end up doing this anyway, assuming a stochastic thermostat. (2/4)

I'm seeing a few neural networks that predict very long molecular dynamics time steps, and I'm not convinced that this is the way to go.

We often want the trajectory not for its own sake, but in order to get snapshots of the underlying ensemble. (1/4)

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...

Now out in JACS! 🎉 : "Computing Solvation Free Energies of Small Molecules with Experimental Accuracy"! It's been a pleasure to collaborate on this with Harry Moore (@jhmchem.bsky.social) & Gábor Csányi pubs.acs.org/doi/10.1021/...

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

Scientific publishing used to be very different, as did science: www.nature.com/articles/248....

GitHub - greener-group/progres: Fast protein structure searching or your money back Fast protein structure searching or your money back - greener-group/progres

The Big Fantastic Virus Database (BFVD) is now available for searching in Progres v1.1.0.

The BFVD is the missing viral bits of the AlphaFold database, and contains a lot of structural diversity.

github.com/greener-grou...

So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵

Exciting news! We have a new website: omsf.io/alchemistry

Your one-stop shop for everything related to our conference community. 🎉

BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event.

Bookmark it as there's plenty more to come!

Congratulations!

Congratulations Nico!

Promising to see open methods for binding free energy prediction improving.

Michel Goedert, sat in front of a computer screen which displays filament fold structures

Excellent opportunity for a #postdoc to join Michel Goedert’s group, investigating the mechanisms which cause the formation of amyloid filaments in neurodegenerative diseases, in collaboration with @sjorsscheres.bsky.social’s group.
More details: www.nature.com/naturecareer...
Closes 04 JAN

National Research Organisations logo, black text on white background surrounded by green and pink lines radiating out from the central text, with Making Research Matter written below

The LMB is proud to be a founding member of the newly launched National Research Organisations (NRO) Group – a new alliance of 35 UK research centres dedicated to #MakingResearchMatter for people, communities & the economy.
Learn more: nrogroup.org
#NROGroup #LMBinthenews

Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have.

mrc.tal.net/vx/mobile-0/...

Kiarash is starting his research group on computational enzyme design, get in touch with him if you want to be part of it.

Embedding space plots for the PDZ protein with Progres and CIRPIN. From Figure 4 in https://www.biorxiv.org/content/10.1101/2025.11.18.689110v1.

Here's a fun visualisation of the embedding space and how the embeddings of proteins related by a circular permutation of the sequence are brought together.

CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs Protein structure-based homology detection has been revolutionized by deep learning methods that can rapidly search massive databases. However, current structural search tools often miss proteins rela...

An interesting study from @aidenkzj.bsky.social, @abulnaga.bsky.social and @sokrypton.org that builds on our Progres model to find pairs of proteins with circular permutations:

www.biorxiv.org/content/10.1...

Proud to share our manuscript:

"How small molecules stabilize oligomers of a phase-separating disordered protein"

www.biorxiv.org/content/10.1...

by Jiaqi Zhu and Tommy Sisk, in collaboration with @borjaml.bsky.social , Stase Bielskute-Garcia & @xsalvatella1.bsky.social

Thanks!