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
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)
We often want the trajectory not for its own sake, but in order to get snapshots of the underlying ensemble. (1/4)
February 4, 2026 at 12:26 PM
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)
We often want the trajectory not for its own sake, but in order to get snapshots of the underlying ensemble. (1/4)
Reposted by Lars Dornfeld
🗓️ 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.
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.
February 3, 2026 at 6:05 AM
🗓️ 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.
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.
Reposted by Lars Dornfeld
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.
January 30, 2026 at 3:42 PM
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.
Reposted by Lars Dornfeld
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
January 22, 2026 at 3:48 PM
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
Reposted by Lars Dornfeld
Another day, another paper describing an ML method for generating conformational ensembles without comparison to any experimental data 😩
January 20, 2026 at 7:45 AM
Another day, another paper describing an ML method for generating conformational ensembles without comparison to any experimental data 😩
Reposted by Lars Dornfeld
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...
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...
GitHub - zoicware/RemoveWindowsAI: Force Remove Copilot, Recall and More in Windows 11
Force Remove Copilot, Recall and More in Windows 11 - zoicware/RemoveWindowsAI
github.com
January 12, 2026 at 6:48 PM
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...
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...
Reposted by Lars Dornfeld
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...
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...
January 12, 2026 at 6:48 AM
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...
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...
Reposted by Lars Dornfeld
Perfect birthday gift 🙌 happy this one is out!
A good end to 2025: rhodamine-binders for bioimaging in JACS: pubs.acs.org/doi/10.1021/...
Fast, Bright, and Reversible Fluorescent Labeling of Rhodamine-Binding Proteins
Rhodamine dyes conjugated to targeting ligands can yield exceptionally bright fluorescent probes for live-cell imaging. However, the limited permeability of such rhodamine derivatives restricts their ...
pubs.acs.org
December 31, 2025 at 2:03 PM
Perfect birthday gift 🙌 happy this one is out!
Reposted by Lars Dornfeld
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
December 26, 2025 at 12:11 PM
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
Reposted by Lars Dornfeld
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🧵👇
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🧵👇
December 16, 2025 at 3:15 PM
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🧵👇
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🧵👇
Reposted by Lars Dornfeld
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...
Théophile Lambert @jsunn-y.bsky.social @francesarnold.bsky.social
www.biorxiv.org/content/10.1...
December 16, 2025 at 12:25 AM
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...
Théophile Lambert @jsunn-y.bsky.social @francesarnold.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Lars Dornfeld
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.
December 12, 2025 at 5:55 PM
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 💡🥳
November 21, 2025 at 11:55 AM
Happy Birthday to our great master student @emma-we.bsky.social - hope you enjoy your life-sized fluorescent protein 💡🥳
Reposted by Lars Dornfeld
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
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!