Simon Dürr
@simonduerr.eu
Assistant Professor UAS at HES-SO Valais-Wallis 🇨🇭 🤗 HF Fellow. Working on AI, Protein Design and Open Science. Creator of bioicons.com
Anyone from the Bio community already got their hands on a NVidia DGX Spark for structure prediction and Protein design workloads ?
October 15, 2025 at 5:43 AM
Anyone from the Bio community already got their hands on a NVidia DGX Spark for structure prediction and Protein design workloads ?
Cool work to design phospho-tyrosine binder by the Baker lab. They show it works but success rate is low (<0.1%) and binders are not super strong (>500nM, likely related to cost of desolvating the phosphate) .
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 1, 2025 at 8:42 AM
Cool work to design phospho-tyrosine binder by the Baker lab. They show it works but success rate is low (<0.1%) and binders are not super strong (>500nM, likely related to cost of desolvating the phosphate) .
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
We are hiring a PhD student 🎓
Work with me and Matthias Rüdt in our department on an exciting industry collaboration with Lonza combining high-throughput experiments and molecular modelling using AlphaFold and MolecularDynamics
📍 Sion, Valais, Switzerland
More info: www.jobup.ch/fr/emplois/d...
Work with me and Matthias Rüdt in our department on an exciting industry collaboration with Lonza combining high-throughput experiments and molecular modelling using AlphaFold and MolecularDynamics
📍 Sion, Valais, Switzerland
More info: www.jobup.ch/fr/emplois/d...
September 25, 2025 at 11:19 AM
We are hiring a PhD student 🎓
Work with me and Matthias Rüdt in our department on an exciting industry collaboration with Lonza combining high-throughput experiments and molecular modelling using AlphaFold and MolecularDynamics
📍 Sion, Valais, Switzerland
More info: www.jobup.ch/fr/emplois/d...
Work with me and Matthias Rüdt in our department on an exciting industry collaboration with Lonza combining high-throughput experiments and molecular modelling using AlphaFold and MolecularDynamics
📍 Sion, Valais, Switzerland
More info: www.jobup.ch/fr/emplois/d...
Interesting work to design antibodies by merging AlphaFold hallucination and an antibody specific language model to design de novo CDR regions in a given antibody framework
🖥️ github.com/SantiagoMill...
🗎 www.biorxiv.org/content/10.1...
🖥️ github.com/SantiagoMill...
🗎 www.biorxiv.org/content/10.1...
September 24, 2025 at 4:03 PM
Interesting work to design antibodies by merging AlphaFold hallucination and an antibody specific language model to design de novo CDR regions in a given antibody framework
🖥️ github.com/SantiagoMill...
🗎 www.biorxiv.org/content/10.1...
🖥️ github.com/SantiagoMill...
🗎 www.biorxiv.org/content/10.1...
Reposted by Simon Dürr
Today we're dropping the "beta" tag from Adaptyv, launching our new website and announcing our $8M seed round.
When we started Adaptyv a few years ago, our core belief was: AI models for biology are only as good as the lab data they're trained on and the hypotheses they can test in the real world.
When we started Adaptyv a few years ago, our core belief was: AI models for biology are only as good as the lab data they're trained on and the hypotheses they can test in the real world.
September 18, 2025 at 5:40 PM
Today we're dropping the "beta" tag from Adaptyv, launching our new website and announcing our $8M seed round.
When we started Adaptyv a few years ago, our core belief was: AI models for biology are only as good as the lab data they're trained on and the hypotheses they can test in the real world.
When we started Adaptyv a few years ago, our core belief was: AI models for biology are only as good as the lab data they're trained on and the hypotheses they can test in the real world.
Reposted by Simon Dürr
🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025
September 17, 2025 at 2:59 PM
🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Reposted by Simon Dürr
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 Simon Dürr
Time to test their claim that diffusion is competitive with hallucination in generating realistic backbones of huge (>800 AA) proteins...
September 11, 2025 at 7:02 PM
Time to test their claim that diffusion is competitive with hallucination in generating realistic backbones of huge (>800 AA) proteins...
La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
September 11, 2025 at 8:23 AM
La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
Ever since Twitter shut down 3rd party clients I sorely missed a client with "remember where I left off" feature. Finally, found a client for Bluesky to do this: @openvibe.social which also supports RSS.
September 11, 2025 at 8:07 AM
Ever since Twitter shut down 3rd party clients I sorely missed a client with "remember where I left off" feature. Finally, found a client for Bluesky to do this: @openvibe.social which also supports RSS.
Reposted by Simon Dürr
Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!
The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬
Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
July 28, 2025 at 3:41 PM
Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!
Reposted by Simon Dürr
Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
July 7, 2025 at 2:21 PM
Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
CC BY is great but also requires that we replace some of our tools. Many currently published CC BY papers are actually not fully CC BY because of BioRender www.chemistryworld.com/news/thousan...
March 19, 2025 at 5:30 PM
CC BY is great but also requires that we replace some of our tools. Many currently published CC BY papers are actually not fully CC BY because of BioRender www.chemistryworld.com/news/thousan...
Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions doi.org/10.1101/2025...
February 10, 2025 at 9:35 AM
Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions doi.org/10.1101/2025...
Reposted by Simon Dürr
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
February 8, 2025 at 9:21 PM
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
Reposted by Simon Dürr
MLSB happening today! Packed room at @neuripsconf.bsky.social East Building Rm 11-12
@workshopmlsb.bsky.social
@workshopmlsb.bsky.social
December 15, 2024 at 5:15 PM
MLSB happening today! Packed room at @neuripsconf.bsky.social East Building Rm 11-12
@workshopmlsb.bsky.social
@workshopmlsb.bsky.social
Reposted by Simon Dürr
Re docking: @workshopmlsb.bsky.social has been piloting a leaderboard for the PLINDER benchmark. It would be awesome to get submissions using existing methods, then everyone can see comparisons better 😁
leaderboard & instructions are on mlsb.io
leaderboard & instructions are on mlsb.io
December 9, 2024 at 4:15 PM
Re docking: @workshopmlsb.bsky.social has been piloting a leaderboard for the PLINDER benchmark. It would be awesome to get submissions using existing methods, then everyone can see comparisons better 😁
leaderboard & instructions are on mlsb.io
leaderboard & instructions are on mlsb.io
Unbelievable how expensive BioRender is. The Max Planck Digital Library is paying 673 413 USD for a two year license for a software that isn't even compatible with open access publishing (even if BioRender claims otherwise). ted.europa.eu/en/notice/-/...
456151-2024 - Result
ted.europa.eu
November 26, 2024 at 1:35 PM
Unbelievable how expensive BioRender is. The Max Planck Digital Library is paying 673 413 USD for a two year license for a software that isn't even compatible with open access publishing (even if BioRender claims otherwise). ted.europa.eu/en/notice/-/...
Now available: open source UI with @Gradio for Boltz-1 by
@gcorso.bsky.social
@jeremywohlwend.bsky.social
Check it out on HuggingFace spaces. h/t
@huggingface.bsky.social
for community L4 GPU: huggingface.co/spaces/simon...
@gcorso.bsky.social
@jeremywohlwend.bsky.social
Check it out on HuggingFace spaces. h/t
@huggingface.bsky.social
for community L4 GPU: huggingface.co/spaces/simon...
Boltz 1 - a Hugging Face Space by simonduerr
Boltz-1
huggingface.co
November 21, 2024 at 8:02 PM
Now available: open source UI with @Gradio for Boltz-1 by
@gcorso.bsky.social
@jeremywohlwend.bsky.social
Check it out on HuggingFace spaces. h/t
@huggingface.bsky.social
for community L4 GPU: huggingface.co/spaces/simon...
@gcorso.bsky.social
@jeremywohlwend.bsky.social
Check it out on HuggingFace spaces. h/t
@huggingface.bsky.social
for community L4 GPU: huggingface.co/spaces/simon...
Gave an intro to Docker + HuggingFace Spaces + Gradio at European Rosettacon 2024 for protein people. Maybe my slides are also interesting to the wider community:
duerrsimon.github.io/docker_huggi...
duerrsimon.github.io/docker_huggi...
Sharing Protein AI Models Using Huggingface - Slidev
Docker + Gradio + Rest API\n
duerrsimon.github.io
November 15, 2024 at 11:00 AM
Gave an intro to Docker + HuggingFace Spaces + Gradio at European Rosettacon 2024 for protein people. Maybe my slides are also interesting to the wider community:
duerrsimon.github.io/docker_huggi...
duerrsimon.github.io/docker_huggi...
Reposted by Simon Dürr
More than 9000 studies published in open-access journals contain figures created using the commercial scientific illustration service BioRender, which should technically mean that they are available for free reuse. But that doesn’t appear to be the case.
www.chemistryworld.com/news/thousan...
www.chemistryworld.com/news/thousan...
Thousands of published studies may contain images with incorrect copyright licences
Questions raised over copyright licence that covers images created using scientific illustration service Biorender
www.chemistryworld.com
October 28, 2024 at 10:49 AM
More than 9000 studies published in open-access journals contain figures created using the commercial scientific illustration service BioRender, which should technically mean that they are available for free reuse. But that doesn’t appear to be the case.
www.chemistryworld.com/news/thousan...
www.chemistryworld.com/news/thousan...