France is switching from Microsoft to Linux "We must become less reliant on American tools and regain control of our digital destiny. We can no longer accept that our data, our infrastructure, our strategic decisions depend on solutions whose rules, pricing, evolution, and risks we do not control."

Such an incredible journey building DISCO 🪩. Love working with this team. DISCO is a co-design model with functional, de novo, new-to-nature enzymes. Huge shoutout to my co-authors for making this a reality! 🚀👇

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...

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 post: blog.escalante.bio/teaching-gen.... You can massively improve in silico metrics for BoltzGen using standard post-training techniques (with a structure model as your reward function). If this holds up (no wetlab testing yet!) you could get binders in seconds rather than hours...

Great opportunity to work on interesting problems in protein design :)

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself. www.science.org/doi/10.1126/...

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)

🗓️ Save the Date! The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹 🗓️ October 28–30, 2026 Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.

Plato's allegory of the cave is so relevant to the natural sciences, yet so many colleagues seem to think they can get away with writing about the shadows.

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

Another day, another paper describing an ML method for generating conformational ensembles without comparison to any experimental data 😩

We love to see it! Community-created harm reduction infrastructure to contest the alarming integration of AI agents into the Windows operating system (which is currently the most reckless deployment environment) ♥️ github.com/zoicware/Rem...

Ever wanted to run MD simulations of entire proteins in water with DFT accuracy? Meet AMPv3-BMS25, the latest iteration of our AMP multiscale neural network potential by @rinikerlab.bsky.social Read more in the preprints: doi.org/10.26434/che... doi.org/10.26434/che...

Perfect birthday gift 🙌 happy this one is out!

Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏

New preprint🚨 Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design? What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be? Why to be wary🧵👇

Finetune a codon-level language model with 30k tryptophan synthases, then generate diverse, functional, enzymes with broad substrate scopes. Théophile Lambert @jsunn-y.bsky.social @francesarnold.bsky.social www.biorxiv.org/content/10.1...

A reminder to use the right P2A sequence to produce separate proteins - the images are from a GPCR-P2A-mCherry construct using a P2A variant without (upper row) and with (lower row) a preceding GSG linker.

Happy Birthday to our great master student @emma-we.bsky.social - hope you enjoy your life-sized fluorescent protein 💡🥳

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

Very happy to be this year’s recipient of the 𝗣𝗲𝘁𝗲𝗿 𝗮𝗻𝗱 𝗧𝗿𝗮𝘂𝗱𝗹 𝗘𝗻𝗴𝗲𝗹𝗵𝗼𝗿𝗻 𝗙𝗼𝘂𝗻𝗱𝗮𝘁𝗶𝗼𝗻 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗔𝘄𝗮𝗿𝗱 together with @jenspuschhof.bsky.social www.engelhorn-stiftung.de/forschungspr...

We figured out flow matching over states that change dimension. With "Branching Flows", the model decides how big things must be! This works wherever flow matching works, with discrete, continuous, and manifold states. We think this will unlock some genuinely new capabilities.

New blog post: Skills for the Future A brief reflection on what skills may (hopefully) remain relevant in the new (hopefully bright) future of LLMs et al. #AcademicWriting #AcademicChatter bastian.rieck.me/blog/2025/sk...

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👇

Are you a PhD student interested in ML and biology or health? Come do an internship with me, @avapamini.bsky.social, Alex Lu, @lcrawford.bsky.social, or Kristen Severson at MSRNE! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/jo...

Yes. Conflating "any data-driven prediction or decision software" with "AI" - a term almost everyone associates with large language models - is a huge gift to the hypemen who claim LLMs will do more energy/climate good than harm. www.techpolicy.press/generative-a...

Congrats @julianvangerwen.bsky.social and rest of the team 🙌

All that my office requires for now is a good tea preparation station

With this, the last bit of my PhD at @embl.org is finally out! We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models. Paper: nature.com/articles/s42256-… Code: github.com/mjendrusch/salad Data: zenodo.org/records/14711580 1/🧵

Really excited to receive the ERC Starting Grant! It’s gonna allow us to do a lot of cool protein design and structural biology method development in the next few years!

Just found this paper during our move. Probably the first one I read about protein design in 2022 😄

We also wrote a little Behind the paper blog post with Lennart and Christian. It gives some idea on what our motivation was behind developing BindCraft and why we chose this particular set of target proteins to work on 🙂 communities.springernature.com/posts/behind...

New blog post: Consciousness Is Overrated Anyway (for AI) In which I, somewhat coherently, try to contribute to the whole "Is AI Conscious" debate. 🔗 bastian.rieck.me/blog/2025/co... #AI #MachineLearning

📢 New preprint: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes. We addressed a long-standing question that people debated already in the 1970s - but it still remained open: Do proteins in crystals move as they do in solution? We used ring flips to find out. 1/n

Should we still teach machine learning classes? Let me justify my existence.

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...

The @uwproteindesign.bsky.social's experimental pipeline behind models like RFdiffusion and ProteinMPNN: - A rapid, scalable, pipeline for producing and characterizing proteins - A demultiplexing protocol for converting oligopools to clonal constructs Jason Qian @lfmilles.bsky.social Basile Wicky

Filtering out homologous structures from the PDB at 40% sequence identity is not enough to create a robust test set. Significant leakage persists at this level, and comparative modeling can still produce high quality models.

🙌

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Our work on rationally engineering allosteric protein switches is now out in Nature Methods: www.nature.com/articles/s41... Thanks a lot to @grunewald.bsky.social and @noahholzleitner.bsky.social for the comprehensive news and views: www.nature.com/articles/s41...

Amazing news! And more than deserved 🙌 looking forward to all your new exciting research - Will be an outstanding lab for PhDs / PostDocs!

Today's #RDKit blog post is a heartfelt plea for clearer communication. greglandrum.github.io/rdkit-blog/p...

Can an AI model predict perfectly and still have a terrible world model? What would that even mean? Our new ICML paper (poster tomorrow!) formalizes these questions. One result tells the story: A transformer trained on 10M solar systems nails planetary orbits. But it botches gravitational laws 🧵

Was an amazing talk @delafuentelab.bsky.social 🙌

BioEmu is out! Grateful to have had the opportunity to work with such an incredible team on this project 🤗

I was involved in this project as an early stage master’s student in protein engineering and it sparked everything that came after 🙌 I’m incredibly grateful I got to work with the amazing supervisor @juliankompa.bsky.social and the rest of the team on such a cool project. Check it out!