ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

Our Garnet paper is now out in final form: a protein and small molecule force field trained from scratch, with competitive results for binding free energy prediction. pubs.rsc.org/sc/article/d...

Joe Greener@jgreener64.bsky.social · 7mo ago

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

Michel Goedert and myself are looking for two postdocs to work on #cryoEM and #masspec of #alphasynuclein filaments from neurodegenerative disease. Come join our bubbly and friendly team at the @mrclmb.ac.uk in lovely Cambridge, UK. www.nature.com/naturecareer...

Postdoctoral Scientist | Neurobiology | Dr Michel Goedert | LMB 2842 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12864505

Postdoctoral Scientist Salary £42,694 per annum Fixed term, 3 years MRC Laboratory of Molecular Biology, Cambridge, UK To work in the group of Dr M...

nature.com

Happy to play a small part in this perspective led by @andreasbender.bsky.social on where AI is in drug discovery, and what we should do in future. www.nature.com/articles/s41... Free link: rdcu.be/fyr77

Artificial intelligence in drug discovery — what it is, where we stand and the path forward - Nature Reviews Drug Discovery

Applications of artificial intelligence (AI) in drug discovery have attracted high interest in recent years, but evidence for clinically relevant impact so far is limited. This Perspective discusses p...

nature.com

1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

Complete Mutagenesis of the Genome and Proteome of ΦX174

The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...

biorxiv.org

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

For non-academic people, this how much UK universities pay publishers to publish their researchers’ articles. The publishers don't pay the researchers, and don't pay the peer reviewers. They also frequently cock up your paper at the typesetting stage. Academic publishing is the worst grift.

Caroline Ball@heroicendeavour.eurosky.social · 2mo ago

Overall data for the UK, by institutional spend. Eye-opening!

Now out as a perspective in PLOS Biology. Where next for structural bioinformatics? journals.plos.org/plosbiology/...

Joe Greener@jgreener64.bsky.social · 12mo ago

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...

I have often seen Microsoft software spread within organisations due to IT and procurement people being "captured" by effective lobbying and sales pitches. Microsoft software is not particularly good, safe or cheap, and researchers benefit from having choice over what they use. @ukri.org

Sjors Scheres@sjorsscheres.bsky.social · 2mo ago

Some inside the @ukri.org wish to push @microsoft.com software too far down into research. This is a risk that didn't work out well for the ICC! @ukri.org should focus on funding good science rather than homogenise for the sake of homogenisation. www.theguardian.com/commentisfre...

Function of a protein: something the protein does. Function in maths: a mapping from X to Y. Function in code: re-use code to do a task. Function at a conference: have a drink and look at posters.

Guardian should ask mathematicians to rank the best 100 numbers. This idea occurred to me as a piss take but it could potentially be good.

Back from parental leave. Thanks to the group for the card, I'm looking forward to the next phase of our science.

Everything you wanted to know about the protein chemistry behind how amino-acid changes affect the cellular abundance of proteins from @tkschulze.bsky.social Effects of residue substitutions on the cellular abundance of proteins doi.org/10.7554/eLif...

This study has been two years in the making and the results have already been widely discussed and compared against, but the paper is finally out in JCIM today! pubs.acs.org/doi/10.1021/...

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE

Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...

pubs.acs.org

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

The LMB Rising Talent Fellowship is open for new applicants! Aimed at Black heritage scientists, the Fellowship offers a 3-year postdoctoral position beginning Oct-Dec 2026. Visit our website for more info: mrclmb.ac.uk/careers-and-... Please circulate this post to anyone who might be interested!

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

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."

Minas Karamanis@minaskar.bsky.social · 6mo ago

Hey, I wrote a thing about AI in astrophysics ergosphere.blog/posts/the-ma...

We have always been overwhelmed by the current data explosion! luispedro.substack.com/p/bioinforma...

Bioinformaticians have been writing the same abstract for decades

We have always been overwhelmed by the data explosion

luispedro.substack.com

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...

Cryo-EM structure of yeast telomerase

YouTube video by MRC Laboratory of Molecular Biology

youtube.com

MRC Laboratory of Molecular Biology@mrclmb.ac.uk · 6mo ago

Led by Investigator Scientist @hongmiaohu.bsky.social, @kellythd-nguyen.bsky.social’s group in the LMB’s Structural Studies Division have produced the first ever structure of telomerase from yeast. Read more here: mrclmb.ac.uk/news-events/... #LMBResearch #cryoEM 🧪

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

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...

arxiv.org

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.

Quanta Magazine@quantamagazine.org · 7mo ago

At the center of every nuclear pore lies a mystery. Here, clumps of proteins wiggle disordered tails around like seaweed. How do they drive a molecular machine that moves so many molecules in and out of the nucleus efficiently, with little room for error? www.quantamagazine.org/disorder-dri...

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...

The one science reform we can all agree on, but we're too cowardly to do

OR: the long overdue forest fire

experimental-history.com

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.