Lars Dornfeld

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

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 😩

GitHub - zoicware/RemoveWindowsAI: Force Remove Copilot, Recall and More in Windows 11 Force Remove Copilot, Recall and More in Windows 11 - zoicware/RemoveWindowsAI

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...

Expression of H1R, H2R and H3R tagged with p2A-mCherry-N1 or p2A2-mCherry-N1 in HELA cells. A) H1R_p2AmCherry-N1 B) H2R_p2AmCherry-N1 C) H3R_p2AmCherry-N1. D, E and F show the H1R, H2R and H3R with p2A2mCherry-N1 respectively.

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...

Quote from the linked article: "Generative AI’s utility in optimizing content for social media algorithms is quite distinct from using real-time algorithms to monitor sensor data about the energy grid. Compressing these numbers into a single category of artificial intelligence is an unfortunate erasure of distinctions that could lead to clearer assessments of generative AI’s impact on productivity."

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...

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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