Lars Dornfeld
@ldornfeld.bsky.social
PhD student in Milles Lab | Passionate about protein design | 🥼&💻 | Formerly with Sereina Riniker (MD), Noelia Ferruz (ML), Bruno Correia (Protein Design) & Kai Johnsson (Protein Engineering)
Webpage: https://ldornfeld.github.io/
Webpage: https://ldornfeld.github.io/
Reposted by Lars Dornfeld
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...
www.engelhorn-stiftung.de/forschungspr...
FORSCHUNGSPREIS — Peter&TraudlEngelhornStiftung
www.engelhorn-stiftung.de
November 14, 2025 at 12:20 PM
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...
www.engelhorn-stiftung.de/forschungspr...
Reposted by Lars Dornfeld
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.
November 10, 2025 at 9:10 AM
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.
Reposted by Lars Dornfeld
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...
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...
Skills for the Future
bastian.rieck.me
November 5, 2025 at 8:46 AM
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...
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...
Reposted by Lars Dornfeld
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👇
October 28, 2025 at 6:30 PM
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👇
Reposted by Lars Dornfeld
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...
Applications are due Dec 1: make sure you include a research statement!
jobs.careers.microsoft.com/global/en/jo...
Search Jobs | Microsoft Careers
jobs.careers.microsoft.com
October 21, 2025 at 7:32 PM
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...
Applications are due Dec 1: make sure you include a research statement!
jobs.careers.microsoft.com/global/en/jo...
Reposted by Lars Dornfeld
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...
www.techpolicy.press/generative-a...
October 14, 2025 at 2:01 PM
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...
www.techpolicy.press/generative-a...
Congrats @julianvangerwen.bsky.social and rest of the team 🙌
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
The functional landscape of the human ubiquitinome
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...
www.biorxiv.org
October 9, 2025 at 2:08 PM
Congrats @julianvangerwen.bsky.social and rest of the team 🙌
Reposted by Lars Dornfeld
All that my office requires for now is a good tea preparation station
October 9, 2025 at 9:31 AM
All that my office requires for now is a good tea preparation station
Reposted by Lars Dornfeld
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/🧵
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/🧵
‘Salad’ – a new AI model from EMBL scientists – offers major improvements in synthetic protein design.
Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.
www.nature.com/articles/s42...
Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.
www.nature.com/articles/s42...
September 24, 2025 at 12:27 PM
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/🧵
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/🧵
Reposted by Lars Dornfeld
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!
📣 The ERC Starting Grant call results are out!
Find out which early-career researchers will receive funding this year, what they will be investigating, where they will be based... plus lots of other #ERCStG facts & figures for 2025!
➡️ buff.ly/IsafuFh
#FrontierResearch 🇪🇺#EUfunded #HorizonEurope
Find out which early-career researchers will receive funding this year, what they will be investigating, where they will be based... plus lots of other #ERCStG facts & figures for 2025!
➡️ buff.ly/IsafuFh
#FrontierResearch 🇪🇺#EUfunded #HorizonEurope
September 4, 2025 at 10:23 AM
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 😄
August 29, 2025 at 5:59 PM
Just found this paper during our move. Probably the first one I read about protein design in 2022 😄
Reposted by Lars Dornfeld
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...
communities.springernature.com/posts/behind...
August 27, 2025 at 9:13 PM
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...
communities.springernature.com/posts/behind...
Reposted by Lars Dornfeld
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
In which I, somewhat coherently, try to contribute to the whole "Is AI Conscious" debate.
🔗 bastian.rieck.me/blog/2025/co...
#AI #MachineLearning
August 24, 2025 at 8:50 PM
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
In which I, somewhat coherently, try to contribute to the whole "Is AI Conscious" debate.
🔗 bastian.rieck.me/blog/2025/co...
#AI #MachineLearning
Reposted by Lars Dornfeld
📢 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
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
August 25, 2025 at 4:38 AM
📢 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
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
Reposted by Lars Dornfeld
Should we still teach machine learning classes? Let me justify my existence.
Just When I Thought I Was Out
They pull me back in! Time to teach machine learning again.
www.argmin.net
August 22, 2025 at 2:30 PM
Should we still teach machine learning classes? Let me justify my existence.
Reposted by Lars Dornfeld
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...
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...
August 15, 2025 at 1:26 PM
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...
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...
Reposted by Lars Dornfeld
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
- 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
August 12, 2025 at 2:34 PM
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
- 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
Reposted by Lars Dornfeld
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.
August 8, 2025 at 7:48 AM
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.
🙌
New drawing!
Ubiquitin-specific protease 7 (pdb 4M5W)
It’s been a while since I last drew anything. Forgot how fun it is.
Ubiquitin-specific protease 7 (pdb 4M5W)
It’s been a while since I last drew anything. Forgot how fun it is.
August 7, 2025 at 10:39 AM
🙌
Reposted by Lars Dornfeld
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🧵
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🧵
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 ...
biorxiv.org
August 5, 2025 at 6:31 AM
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🧵
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🧵
Reposted by Lars Dornfeld
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...
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.
www.nature.com
August 4, 2025 at 11:41 AM
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!
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
July 25, 2025 at 9:04 AM
Amazing news! And more than deserved 🙌 looking forward to all your new exciting research - Will be an outstanding lab for PhDs / PostDocs!
Reposted by Lars Dornfeld
Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Please stop saying “The Tanimoto similarity is” – RDKit blog
A simple tip to explain what you actually did
greglandrum.github.io
July 17, 2025 at 11:22 AM
Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Reposted by Lars Dornfeld
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 🧵
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 🧵
July 14, 2025 at 1:50 PM
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 🧵
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 🙌
Excited to have participated in the 2025 Symposium on Generative AI in Molecule Discovery in beautiful Munich, along with amazing scientists and colleagues @machine.learning.bio, Francesca Grisoni, @ewaszczurek.bsky.social, @fabiantheis.bsky.social and more... 🔬🤖 events.hifis.net/event/2015/
July 11, 2025 at 8:41 AM
Was an amazing talk @delafuentelab.bsky.social 🙌