iiinova — where your digital self keeps evolving

Reposted by Simon Dürr

Helena Klara Jambor @helenajambor.bsky.social · 10/09/2026

Very happy about this months #PointsOfView in #NatureMethods - The Graphical Abstract. Co-authored with @simonduerr.eu, with whom I share a long-time passion for #Icons #BioIcons and #CC0 figures - and fuelled by our joint workshop for the @sib.swiss at [BC]2! Here is a 🎁 link lnkd.in/e5ew-E2R

Four ways to use a graphical abstract, as table of content icon, on social media, in talks and on posters.

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Reposted by Simon Dürr

Gina El Nesr @ginaelnesr.bsky.social · 28/04/2026

Excited to report the first zero-shot designed, de novo enzyme catalyzing two of the most energetically demanding reactions in biology—phosphomonoester and phosphodiester hydrolysis—with catalytic efficiencies comparable to natural enzymes! 🚀 /🧵 @stanfordbiosci.bsky.social @simonduerr.eu

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Reposted by Simon Dürr

jproney @jproney.bsky.social · 12/12/2025

As a bonus, here's a video of ProteinEBM folding up the fast-folder NTL9, rendered in stunning 2D by py2Dmol from @sokrypton.org! We hope models like ProteinEBM can serve as a step toward solving the "real" protein folding problem.

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Simon Dürr @handle.invalid · 15/10/2025

Anyone from the Bio community already got their hands on a NVidia DGX Spark for structure prediction and Protein design workloads ?

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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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Reposted by Simon Dürr

adaptyv.bio @adaptyv.bio · 18/09/2025

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.

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Reposted by Simon Dürr

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 17/09/2025

🚨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.

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Reposted by Simon Dürr

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025

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💫

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Reposted by Simon Dürr

Diego del Alamo @delalamo.xyz · 11/09/2025

Time to test their claim that diffusion is competitive with hallucination in generating realistic backbones of huge (>800 AA) proteins...

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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 · 11/09/2025

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.

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Reposted by Simon Dürr

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 28/07/2025

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

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Reposted by Simon Dürr

Gina El Nesr @ginaelnesr.bsky.social · 07/07/2025

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…

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Simon Dürr @handle.invalid · 19/03/2025

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...

chemistryworld.com

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

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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...

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Sri Kosuri @srikosuri.bsky.social · 08/02/2025

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.

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Reposted by Simon Dürr

Gina El Nesr @ginaelnesr.bsky.social · 15/12/2024

MLSB happening today! Packed room at @neuripsconf.bsky.social East Building Rm 11-12 @workshopmlsb.bsky.social

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Reposted by Simon Dürr

Hannah Wayment-Steele @hkws.bsky.social · 09/12/2024

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

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Simon Dürr @handle.invalid · 26/11/2024

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/-/...

ted.europa.eu

456151-2024 - Result

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Simon Dürr @handle.invalid · 21/11/2024

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...

huggingface.co

Boltz 1 - a Hugging Face Space by simonduerr

Boltz-1

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Simon Dürr @handle.invalid · 15/11/2024

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

Sharing Protein AI Models Using Huggingface - Slidev

Docker + Gradio + Rest API\n

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Reposted by Simon Dürr

Chemistry World @chemistryworld.com · 28/10/2024

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...

chemistryworld.com

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

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