"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."

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...

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...

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

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.

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.

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!

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.

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

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...

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/...

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 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

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...

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...

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-...

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.

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

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...

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

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.

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...