Thanks Martin!
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.
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.
I can overlook millimetres per year, but what utter anarchy of a unit is inches per megasecond
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)
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/...
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....
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.
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
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.
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.
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
