Arne Schneuing
@rne.bsky.social
PhD student @EPFL 🇨🇭
ML & computational biology 🤖🧬⚛️
ML & computational biology 🤖🧬⚛️
Pinned
Arne Schneuing
@rne.bsky.social
· Mar 7
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
Reposted by Arne Schneuing
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Reposted by Arne Schneuing
You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
September 12, 2025 at 12:43 PM
You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
Reposted by Arne Schneuing
Nature research paper: One-shot design of functional protein binders with BindCraft
go.nature.com/46bhOAv
go.nature.com/46bhOAv
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
go.nature.com
September 1, 2025 at 5:37 PM
Nature research paper: One-shot design of functional protein binders with BindCraft
go.nature.com/46bhOAv
go.nature.com/46bhOAv
Reposted by Arne Schneuing
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Arne Schneuing
@aithyra.bsky.social Opening Symposium "AI for Life Science" with Nobel Laureate Frances Arnold as keynote speaker in addition to an outstanding line up of speakers on a variety of topics across biological scales and data modalities.
Registration is now open at cemm.at/aithyra-symp...
Registration is now open at cemm.at/aithyra-symp...
July 24, 2025 at 7:26 PM
@aithyra.bsky.social Opening Symposium "AI for Life Science" with Nobel Laureate Frances Arnold as keynote speaker in addition to an outstanding line up of speakers on a variety of topics across biological scales and data modalities.
Registration is now open at cemm.at/aithyra-symp...
Registration is now open at cemm.at/aithyra-symp...
Reposted by Arne Schneuing
BioEmu now published in @science.org !!
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
July 10, 2025 at 6:57 PM
BioEmu now published in @science.org !!
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
BioEmu is out! Grateful to have had the opportunity to work with such an incredible team on this project 🤗
Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...
July 10, 2025 at 8:00 PM
BioEmu is out! Grateful to have had the opportunity to work with such an incredible team on this project 🤗
Reposted by Arne Schneuing
BioEmu is now on @science.org ! The revised version includes an upgraded model and makes a lot of MD simulation data internally generated at MSR available to the public. This took a lot of firepower from us in the last two years.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Scalable emulation of protein equilibrium ensembles with generative deep learning
Following the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu, a deep learning system that...
www.science.org
July 10, 2025 at 6:09 PM
BioEmu is now on @science.org ! The revised version includes an upgraded model and makes a lot of MD simulation data internally generated at MSR available to the public. This took a lot of firepower from us in the last two years.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Arne Schneuing
New research in Science greatly expands the potential target scope of molecular glues and should stimulate the development of new small molecules that can selectively target therapeutically relevant proteins for degradation.
Learn more in this week's issue: scim.ag/44uRorm
Learn more in this week's issue: scim.ag/44uRorm
July 3, 2025 at 6:05 PM
New research in Science greatly expands the potential target scope of molecular glues and should stimulate the development of new small molecules that can selectively target therapeutically relevant proteins for degradation.
Learn more in this week's issue: scim.ag/44uRorm
Learn more in this week's issue: scim.ag/44uRorm
Reposted by Arne Schneuing
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
github.com/martinpacesa...
Reposted by Arne Schneuing
Please welcome AITHYRA, the Research Institute for Artificial Intelligence of the Austrian Academy of Science on social media. Follow us and connect via Bluesky and LinkedIn 👋
April 28, 2025 at 7:44 AM
Please welcome AITHYRA, the Research Institute for Artificial Intelligence of the Austrian Academy of Science on social media. Follow us and connect via Bluesky and LinkedIn 👋
Reposted by Arne Schneuing
Hello from Singapore 🇸🇬! Thrilled to be at #ICLR2025 presenting our work on fragment-based drug discovery 🧩. We go beyond virtual screening with a generative, structure-aware approach.
📃 openreview.net/forum?id=bZW...
🔗 github.com/rneeser/Late...
A thread 🧵👇
📃 openreview.net/forum?id=bZW...
🔗 github.com/rneeser/Late...
A thread 🧵👇
Flow-Based Fragment Identification via Contrastive Learning of...
Fragment-based drug design is a promising strategy leveraging the binding of individual fragments, potentially yielding ligands with multiple key interactions, surpassing the efficiency of full...
openreview.net
April 24, 2025 at 7:13 AM
Hello from Singapore 🇸🇬! Thrilled to be at #ICLR2025 presenting our work on fragment-based drug discovery 🧩. We go beyond virtual screening with a generative, structure-aware approach.
📃 openreview.net/forum?id=bZW...
🔗 github.com/rneeser/Late...
A thread 🧵👇
📃 openreview.net/forum?id=bZW...
🔗 github.com/rneeser/Late...
A thread 🧵👇
Reposted by Arne Schneuing
📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs.
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
April 11, 2025 at 2:47 PM
📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs.
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
Reposted by Arne Schneuing
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Google Colab
colab.research.google.com
March 29, 2025 at 9:50 AM
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Reposted by Arne Schneuing
I’m looking for a BTA and a Postdoc to help set up the Structural Biochemistry group at the Leibniz Institute for Immunotherapy (LIT) in Regensburg 😀.
We apply synthetic biology and protein design to address key challenges in immunotherapy.
lit.eu/work-with-us/
#SynBio #ProteinDesign #Immunotherapy
We apply synthetic biology and protein design to address key challenges in immunotherapy.
lit.eu/work-with-us/
#SynBio #ProteinDesign #Immunotherapy
Work With Us
The LIT welcomes individuals from all life paths and academic backgrounds. If you are passionate about science we could be the perfect home for you.
lit.eu
March 13, 2025 at 2:50 PM
I’m looking for a BTA and a Postdoc to help set up the Structural Biochemistry group at the Leibniz Institute for Immunotherapy (LIT) in Regensburg 😀.
We apply synthetic biology and protein design to address key challenges in immunotherapy.
lit.eu/work-with-us/
#SynBio #ProteinDesign #Immunotherapy
We apply synthetic biology and protein design to address key challenges in immunotherapy.
lit.eu/work-with-us/
#SynBio #ProteinDesign #Immunotherapy
Reposted by Arne Schneuing
🚨 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
Additional details in thread 🧵
#ICLR2025
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
March 11, 2025 at 3:02 PM
🚨 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
Additional details in thread 🧵
#ICLR2025
Reposted by Arne Schneuing
Introducing All-atom Diffusion Transformers
— towards Foundation Models for generative chemistry, from my internship with the FAIR Chemistry team
There are a couple ML ideas which I think are new and exciting in here 👇
— towards Foundation Models for generative chemistry, from my internship with the FAIR Chemistry team
There are a couple ML ideas which I think are new and exciting in here 👇
March 10, 2025 at 4:20 PM
Introducing All-atom Diffusion Transformers
— towards Foundation Models for generative chemistry, from my internship with the FAIR Chemistry team
There are a couple ML ideas which I think are new and exciting in here 👇
— towards Foundation Models for generative chemistry, from my internship with the FAIR Chemistry team
There are a couple ML ideas which I think are new and exciting in here 👇
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
March 7, 2025 at 1:38 PM
The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
📚 Paper: openreview.net/forum?id=g3V...
💻 Code: github.com/LPDI-EPFL/Dr...
(1/4)
Reposted by Arne Schneuing
The BioEmu-1 model and inference code are now public under MIT license!!!
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
February 19, 2025 at 8:17 PM
The BioEmu-1 model and inference code are now public under MIT license!!!
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
Reposted by Arne Schneuing
We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!
January 19, 2025 at 12:15 PM
We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!
Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia!
t.co/vtYlhi8aQm
t.co/vtYlhi8aQm
January 15, 2025 at 4:37 PM
Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia!
t.co/vtYlhi8aQm
t.co/vtYlhi8aQm
Reposted by Arne Schneuing
Awesome paper!
BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1...
Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1...
Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
January 12, 2025 at 5:22 PM
Awesome paper!
BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1...
Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1...
Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg
Reposted by Arne Schneuing
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Structure-based drug design with equivariant diffusion models - Nature Computational Science
This work applies diffusion models to conditional molecule generation and shows how they can be used to tackle various structure-based drug design problems
www.nature.com
December 9, 2024 at 2:00 PM
After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Arne Schneuing
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 6, 2024 at 8:39 AM
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...