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

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

Our #tutorial on how to make @plumed.org faster is now published in @acs.org #JPCB! doi.org/10.1021/acs.... Preprint and summary in previous thread: bsky.app/profile/buss...

No joke: I got angry hate mail today for writing an obituary of a Black woman scientist—because the person felt she did didn’t deserve the recognition. Which just makes me want to share it again: www.nature.com/articles/d41...

Can proteins fold and function with half of the amino acid alphabet? Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved. A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v #ProteinDesign #OriginsOfLife

Download it here: www.tandfonline.com/eprint/DUBR5...

Electric field-induced destabilization and surface modulation of Aβ42 fibrils in molecular simulations: theoretical implications for direct current stimulation in Alzheimer’s disease www.tandfonline.com/doi/full/10....

Excited to see this work on the cover of #MolecularCell. A massive, open #cryoEM #cryoET dataset capturing molecular organization inside intact cells, pushing what’s possible for #visualproteomics, method development, and computational reuse. Congratulations to the authors. ter.li/of4cgh

Targeting the histone‐fold dimerization interface of oocyst rupture proteins from Plasmodium berghei for antimalarial inhibitor discovery - Ballabio - The FEBS Journal - Wiley Online Library febs.onlinelibrary.wiley.com/doi/full/10....

RE: https://mastodon.online/@Centre_Mersenne/115661990703325565 Society journals adopting the diamond open access model with financial support from science funding bodies and research institutions is a key step towards getting us out of the mess academic publishing currently is. This is […]

I just published: ERC-Plus: jackpot science or missed chance to fix academia? My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re building. medium.com/p/erc-plus-j...

All data are available on Zenodo and we'd love to see what you can do with it! Cydney also made a nice notebook to run the predictive model (including DMS scan) in Colab! Preprint: biorxiv.org/content/10.1... Colab: colab.research.google.com/drive/1KNWvG... Data: docs.google.com/forms/d/e/1F...

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

I fully endorse this. Political leaders are falling prey to AI hype, and seem to lack any kind of help from reputable sources who could counter the false claims of tech CEOs. Where are their science advisers???

The idea is to decouple the journals from the review step. They’ll still exist, but they’ll need to add other value. They’ll highlight, curate, add new perspectives. If they do a good job they can still be prestigious (like Scientific American or Wired) (1.2) 👇

A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699

It’s official: ChatGPT can't draw a GPCR, but you’ll master them in the Filizola Lab 😜 Join Us! (send your CV and the names of at least two references to my institutional email) #Postdoc #scientist #research

I'm hiring for a PhD position at Malmö University, Sweden! The project will focus on molecular modelling of proteins, lipids, and biomolecular condensates at cell membranes. More details and application form: tinyurl.com/4zm92365 Please feel free to share! @vetenskapsradet.bsky.social | @mau.se

We asked what a strong static EF may do to AB42 fibril, we saw a marked perturbation of the fuzzy coat and increase fluctuations of the fibril core

Apple is entering the protein folding arena. SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

RFdiffusion3 is here! We train a general network that explicitly models every atom and use it to design active enzymes and DNA binders. Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others! Check it out: lnkd.in/eiUFfJaM.

AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`! AtomWorks: github.com/RosettaCommo... RF3: github.com/RosettaCommo... Paper: tinyurl.com/y2w4z65b 1/6

RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...

🚀 Super excited to share our new work, led by @vschnapka.bsky.social bAIes, a Bayesian framework for generating accurate atomic-resolution ensembles of IDPs using #AlphaFold info! Now on @biorxivpreprint.bsky.social → feedback welcome! @pasteur.fr @erc.europa.eu www.biorxiv.org/content/10.1...

the JIF 👇 is a very (!) narrow definition of "impact" = cites in first 2y after publication... 👉 What about "constant" or "late" impact? 👉 Why do we accept that a private company defines our impact? 👉 Why do we allow to be judged on this basis? #researchintegrity #chemsky, #compchemsky

Rapid, nanoscale dynamics of individual IDPs determine bulk properties of the entire condensate, such as viscosity. Amazing work by Nicola Galvanetto & the Schuler lab! www.pnas.org/doi/10.1073/...

Congratulations to Michele Parrinello for receiving the ESI Medal 2025! @esivienna.bsky.social @univie.ac.at

Choose Science. Choose Europe. A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open. With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond. Apply by 10 September → europa.eu/!fBTMgF

What an incredibly cool paper! While knot theory strictly applies to closed curves, Tommy, @smnlssn.bsky.social , and @paulrobustelli.bsky.social show that writhe, a knot "non-invariant" that changes with smooth deformations, provides a meaningful descriptor for flexible conformations.

onlinelibrary.wiley.com/doi/10.1002/... Federico did some modeling to make some hypothesis on the interaction of anthocyanin with glucose transporter

Protein folding, binding and redox conditions by Stefano Gianni team in Rome the super productive Valeria Pennacchietti, doi.org/10.1016/j.ij...

Very proud of Amit Kumawat, Elisa Tavazzani and all coworkers for this work on hERG K+ channel rescue mechanism by ICA. Now published here: jbiomedsci.biomedcentral.com/articles/10....

A single python package for calculation of quality metrics like DockQ, LDDT, RMSD, & others peppr.vant.ai

Very true!

Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations. Thanks @jjimenezluna.bsky.social for the help! 🌐 colab.research.google.com/github/sokry... 📄 www.biorxiv.org/content/10.1...

We’re looking for fellow nerds to help us make disordered proteins druggable. Love #IDPs, #MD, #NMR, #AI, #DrugDiscovery, or #MassSpec? Let’s talk. @bindresearch.org is hiring across the board: bindresearch.org/careers/ #compchem #compbio #NMRChat #TeamMassSpec #chemjobs @chemjobber.bsky.social

Structural bases for Nuclear Factor 1-X activation and DNA recognition. Prototypic insight into the NFI transcription factor family https://www.biorxiv.org/content/10.1101/2025.03.21.644642v1

Structural bases for Nuclear Factor 1-X activation and DNA recognition. Prototypic insight into the NFI transcription factor family https://www.biorxiv.org/content/10.1101/2025.03.21.644642v1

I missed this when it came out. (Or I’ve forgotten it. Hard to know which… 😄) Either way, perhaps the future is more research alliances with Europe? (And away from the US.) NZ is associated to pillar 2 of the Horizon programme: research-and-innovation.ec.europa.eu/strategy/str...

ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...

The paper describing our community effort to collect and organize #plumed tutorials has been published in the Journal of Chemical Physics, as part of the Michele Parrinello Festschrift! doi.org/10.1063/5.02...

In this world of shrinking research budgets, academic layoffs and failing universities, Elsevier is still making an obscene profit. If anything has radicalised me to green it's these numbers. www.researchprofessionalnews.com/rr-news-worl...

It is with sadness I share that my long-term collaborator and friend prof. Per Jemth passed away last week after a short time of illness. He is greatly missed.

We are building high-throughput tools and public datasets to make disordered proteins druggable for everyone. Want to drug the undruggable with us? We’d love to hear from you! Reach out at bindresearch.org.

We’re thrilled to announce the launch of Bind Research, the UK’s first not-for-profit Focused Research Organisation, with long-term support from the Department for Science, Innovation and Technology’s Research Ventures Catalyst Programme, industry, and charities.

Published in JCIM, #compchem pubs.acs.org/doi/full/10....

Continuing the peer review discussion: @katherine-brown.bsky.social on principles for effective peer review: 1) Be respectful to authors 2) Request reasonable revisions 3) Focus on whether data support the conclusions 4) Be transparent about expertise limits thenode.biologists.com/peer-review-...

📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org