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!

Happy to announce that our paper, "ProtMamba: a homology-aware but alignment-free protein state space model", has been published in Bioinformatics! 🎉 doi.org/10.1093/bioi...

We will be hosting a mirror site of the CASP data and workflows at @sib.swiss. Operating a redundant site with independent funding is a good idea for important scientific infrastructure, independent from the current funding situation in the US.

I had the honor of receiving both the Otto Hahn Medal and Award of the May Planck Society. I am looking forward to transforming this chance into an own research group pushing the boundaries of interdisciplinary phage research! Huge thanks to all colleagues, collaborators, family and friends!

🧪 New preprint: "Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings" We generate complete, all-atom protein conformational ensembles, capturing both backbone and side-chain dynamics of, e.g., the Dopamine D2 receptor. arxiv.org/abs/2506.17064

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

Excited to share my main PhD work is finally out! 🥳 We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)! See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞

An improved model for prediction of de novo designed proteins with diverse geometries https://www.biorxiv.org/content/10.1101/2025.06.02.657515v1

🚀 Excited to release BoltzDesign1! ✨ Now with LogMD-based trajectory visualization. 🔗 Demo: rcsb.ai/ff9c2b1ee8 Feedback & collabs welcome! 🙌 🔗: GitHub: github.com/yehlincho/Bo... 🔗: Colab: colab.research.google.com/github/yehli... @sokrypton.org @martinpacesa.bsky.social

Two more🙃: 1) arxiv.org/abs/2412.12979 2) arxiv.org/abs/2505.15093

Protein design and optimization for synthetic cells

Enjoy @julianvangerwen.bsky.social!

"Adapting ProteinMPNN for antibody design without retraining" Our several-years-old fix to ProteinMPNN's tendency to make weird antibody CDR sequences is finally preprinted

Inverse folding NNs are better at predicting changes to a mutated protein's equilibrium dynamics, relative to WT, than protein folding NNs (BioEmu & AF-Cluster). This was shown on an enzyme that is more enzymatically promiscuous in the open state.

Reading group tomorrow: @json_yim and @woodyahern present "Atom level enzyme active site scaffolding using RFdiffusion2" www.biorxiv.org/content/10.1... Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

TFW you realize that you built a *bunch* of models using sklearn's RandomForestRegressor using default params, which, of course, means that you didn't actually build random forests. 🤦 Ah well, they don't take that long to build and the real random forests build even faster.

Preprint from the lab🚨 Have you ever engineered proteins to be more stable and were unhappy about your predictor's success rate? We got you covered with BoostMut! Great work led by @kerlenkorbeld.bsky.social now online at www.biorxiv.org/content/10.1... A thread 🧵

I think a lot about what Carl Sagan said in one of his final interviews.

Excited to present my first paper officially as a PhD student now as an ICLR Oral this week! Super fun work with the GenAIR team at NVIDIA. Talk: Fr 10:54 - 11:06 (Oral Session 3B, Garnet 213-215) Poster: Fr 15:00-17:30 (Hall 3 + Hall 2B #5) Come by the poster/reach out to chat

Some crystal structures show evidence of multiple stable conformations, such as loops or side chains with two distinct regions of density. These can be correctly modeled by MD, but not modern protein ensemble prediction tools like AlphaFlow or DiG (BioEmu not tested) www.biorxiv.org/content/10.1...

Job alert: Join us in Mainz as Max Planck Research Group Leader (W2) in Molecular Design ...and make your own research dreams happen on de novo design, generative models, proteins, materials ... tinyurl.com/r2xjxnuk @mpip-mainz.mpg.de

Cool opportunity for people searching for PhD out there :)

Love it 😂

🎉Congrats to Chase on her new preprint! She developed OMEGA--a simple method for assembling custom gene panels for as little as $1.50 per gene. Big step forward protein engineering and design!🧬 www.biorxiv.org/content/10.1...

What an amazing experience to be at the 76th Mosbacher kolloquim! Awesome talks on protein design and structural biology and a lot of conceptual discussions on where the field is going. Glad to also have been able to present our poster on binder design using BindCraft!

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics? @hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1! 🧵

🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly! Additional details in thread 🧵 #ICLR2025

Such a fun project to work on with a stellar team! Stay tuned for other things to come here, and see you all in Singapore!

I’m happy to share that I will join the LIT in Regensburg (lit.eu) as a Group Leader in Structural Biochemistry in May. We will combine synthetic biology and protein design to develop synthetic receptors and protein therapeutics to improve immunotherapy. Job openings will be available soon!

Great to see this out, congrats to the lab!🎉