Lars Dornfeld

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
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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...

To briefly summarize my argument (cf. Orwell): When you are being stomped on by a boot, it does not matter whether the wearer is a conscious entity and capable of reflection. It just hurts.

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.
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Just When I Thought I Was Out They pull me back in! Time to teach machine learning again.

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

Scatter plot of LDDT as a function of sequence identity for high coverage homology models. The horizontal red line at 40% sequence identity highlights the presence high quality models in the low sequence identity region.

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.

🙌

Scaling down protein language modeling with MSA Pairformer Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

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🧵

Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites - Nature Methods ProDomino is a machine leaning-based method, trained on a semisynthetic domain insertion dataset, to guide the engineering of protein domain recombination.

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 🧵

A good example of unfolding „cat“alysis

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

Joe Greener

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 🌚🌞

For me as well 🥲