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Simon Dürr

@simonduerr.eu
1.8K followers 1.3K following 66 posts

Assistant Professor UAS at HES-SO Valais-Wallis 🇨🇭 🤗 HF Fellow. Working on AI, Protein Design and Open Science. Creator of bioicons.com

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Simon Dürr @handle.invalid · 04/02/2026
Curious to try it but it will probably still be unusable if you care about the things you want to illustrate. There is already some services that wrap NanoBananaPro for Figure generation and even the teaser images they show are wrong: For example grabstract.io
Carbons with 5 bonds in AI generated images.
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Simon Dürr @handle.invalid · 16/10/2025
Great. Would be nice to have a more direct comparison of the same pipeline on different hardware. If one has to specially optimize each model (TensorRT, BF16) its clearly an argument to stick with an x86 machine
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Simon Dürr @handle.invalid · 01/10/2025
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...
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Simon Dürr @handle.invalid · 25/09/2025
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...
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Simon Dürr @handle.invalid · 24/09/2025
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...
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Simon Dürr @handle.invalid · 11/09/2025
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
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Simon Dürr @handle.invalid · 21/02/2025
Installation and running it was a breeze 🤗 Diversity of the generated structures is quite good. Quality is a bit hit and miss. Most samples at default params have at least one or two weird C-N peptide bonds >1.6A/<1.1A and also had a few (<0.5%) samples with quite severe clashes.
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Simon Dürr @handle.invalid · 10/02/2025
We've made available a ChimeraX extension and a Webapp to easily run predictions. AllMetal3D is now also easily installable using pip. ChimeraX: cxtoolshed.rbvi.ucsf.edu/apps/chimera... HuggingFace: huggingface.co/spaces/simon... Docs for Python Package: lcbc-epfl.github.io/allmetal3d/
ChimeraX preview
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Simon Dürr @handle.invalid · 10/02/2025
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...
Performance of AllMetal3D vs. Metal3d.
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Simon Dürr @handle.invalid · 22/12/2024
In the fictional universe of the BioRender lawyers they can claim they are compatible with CC BY but fact is the figures created in BioRender cannot be reused under CC BY because they say one needs a paid account which is against the CC BY terms (compare BioRender vs. @creativecommons.bsky.social).
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