Exploiting internal symmetry can be a powerful approach to analyse convergence in MD simulations.

If two conformational states are symmetry related, their kinetic and thermodynamic properties should be the same. If one doesn't enforce this during analysis this provides a useful test. 1/n

Women scientists look at sample

Been away from scientific research for over a year and want to get back to the bench?

LMB's new Career Returner Fellowship bridges the gap for those who want to re-enter lab-based research.

Applications open 13 April

More info mrclmb.ac.uk/careers-and-...

PLEASE SHARE THIS!
@mrclmb.ac.uk

"Every hour you spend confused is an hour you spend building the infrastructure inside your own head that will eventually let you do original work."

Bioinformaticians have been writing the same abstract for decades We have always been overwhelmed by the data explosion

We have always been overwhelmed by the current data explosion!

luispedro.substack.com/p/bioinforma...

i'm so sorry we've sent these souls to the moon and they're using outlook?

On this 1st April I'm happy to release a technical report from our startup MirageBio, describing a new protein structure model with state-of-the-art performance.

jgreener64.github.io/posts/techni...

Job opening for Scientific Computing Officer at MRC Laboratory of Molecular Biology focussing on HPC and hands-on open-source computing to support research.

Join our Scientific Computing team!
Work with open source HPC systems, support Linux/Mac/PC environments, script smart solutions & help build in house tech. Great for a curious, creative problem solver.
www.nature.com/naturecareer...
Apply by 19 APR
#ComputingJobs #CambridgeJobs #Hiring

Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍.
www.science.org/doi/10.1126/...
www.youtube.com/watch?v=gFE4...

This marks the first paper from the group proper. Well done to Alexandre Blanco-González, @tkschulze.bsky.social and Evianne Rovers for making it so great. (4/4)

GitHub - greener-group/garnet: Garnet biomolecular force field Garnet biomolecular force field. Contribute to greener-group/garnet development by creating an account on GitHub.

Training on quantum mechanical and experimental data was essential for learning the weak van der Waals interactions.

The method and force field are available under a permissive licence at github.com/greener-grou.... (3/4)

An overview of the Garnet model architecture.

An automated, reproducible training pipeline means we can assess different functional forms.

We found that the double exponential potential was accurate and easier to train than the typical Lennard-Jones potential. (2/4)

Training a force field for proteins and small molecules from scratch Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural networ...

Check out our pre-print, where we train a protein and small molecule force field from scratch with a graph neural network.

We show comparable performance to existing, manually-tuned force fields on a range of tasks including binding free energy prediction. (1/4)

arxiv.org/abs/2603.16770

arXiv is separating from Cornell University and the Simons Foundation to become an independent non-profit.

They are advertising for a CEO whose salary will take ~5% of the budget: jobs.chronicle.com/job/37961678....

I just hope they can maintain the efficient model that has worked well for years.

Interesting article and visualisations. Hopefully one day we can run all-atom simulations of the nuclear pore.

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk

Thanks Martin!

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