Simon Duerr

More info via this link or via DM jobup.ch/fr/emplois/det…

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

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 experimental data they're trained on and the hypotheses they can test in the real world. Now, after a year of working with many great partners, we’ve scaled our infrastructure to the point that we're now open to anyone who wants to use our platform! Overall, this year, over 30 companies started using Adaptyv to validate their protein designs - from some of the biggest pharmas to frontier AI labs to many, many techbio startups. We've run hundreds of experiments, tested well over 10,000 proteins this year and are generating the data that validates the best AI models currently in development.

Chai Discovery just released their new model Chai-2, validated on Adaptyv! Chai-2 enables generation of de novo proteins and epitope-specific antibodies using a multimodal generative architecture that integrates all-atom structure prediction and generative modeling. Chai tested many of their new protein designs using our high-throughput wet lab at Adaptyv to get high quality data to improve their AI models in as little as two weeks per round.

@sokrypton I really like uberspace.de Managed Hosting with ssh access.

Any suggested PHP+MySQL hosting platforms? In the past I've used Bluehost, but recently they've been getting more and more restrictive.

In earlier work, we already analyzed how AllMetal3D given a structural input and no information about metal stoichiometry fares against co-folding methods given metal stoichiometry but no structure: doi.org/10.1101/2024.0…

We compared to a few other tools that perform either metal identity prediction or location prediction and found that is very important to include negative classes during training and also cluster metal ions by biological similarity.

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/10.1101/2025.0…

@anjbth @NIAIDNews No. The icons come with the very permissive CC0 license . You can basically do what you want ( even without providing credit). It is however appreciated to credit NIAID

@simonduerr @NIAIDNews Any copyright concern? Licencing needs?

This is great! @NIAIDNews have launched a collection of public domain illustrations (currently 550 individual icons) bioart.niaid.nih.gov

@a19grey @david_koes Smiles is 2D, you need to generate a conformer (e.g using rdkit) to get 3d coordinates which you can then visualize using molecule3d

@simonduerr @david_koes Thanks! Am i doing something wrong? I just want a cute little 3D water molecule.

First beta release of a native Molecule viewer for Gradio built on 3dmol.js: Gradio Molecule3D Simply install it using pip install gradio_molecule3d 1/3

@a19grey @david_koes Use this for smiles strings huggingface.co/spaces/simondu…

@simonduerr @david_koes Thanks! I was hoping to use this to display general molecules like H2 or LiH but seems I can't do general SMILES format molecules using this library?

Thank you to everyone who came to MLSB this year!! We are collecting feedback in a short 2 minute survey (and more data means maybe next year we'll train a new model... or just get a bigger room 😄) forms.gle/WHFNfvxVh3QxuT…

@THE_inteins @MPDL For sure! Also you could buy 5000 images at a cost of 124 $ each for this money and use them anywhere you want instead of only being able to edit them in their webapp.

@simonduerr @MPDL One one hand, I get it, BioRender is convenient. On another, almost $700K/2-year license for soulless images that looks like they were copied 700 times from one publication into another is insane!

Unbelievable how expensive BioRender is. @MPDL 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/-/de…

Anyone working at MPG willing to share the license conditions ? I'd be curious if they have special terms. For the last contract they didn't. The info should be on this page: soli.mpdl.mpg.de/en/software/bi…

@anthonygitter Can you try without special characters? I'll take a look

@simonduerr It worked a couple times but now I'm still getting errors "failed with error:[Errno 2] No such file or directory: 'test-predict/boltz_results_test-predict/predictions/test-predict/'" for job name "test-predict"

Now available: open source UI with @Gradio for Boltz-1 by @GabriCorso @jeremyWohlwend Check it out on HuggingFace spaces. h/t @huggingface for community L4 GPU: huggingface.co/spaces/simondu…

@anthonygitter Oh this shouldn't happen. Fix is pushed.

@simonduerr Thanks for making this! What does it mean if the output shows Error? This was with the Top7 example input.

@ClementDelangue @GabriCorso Boltz-1 now also available on HF Spaces. Gradio made this very easy :) x.com/simonduerr/sta…

Give this some love - open-source biology AI needs more recognition! huggingface.co/boltz-communit… by @GabriCorso and team

Note that this is an Alpha release. It will soon be also possible to define modified residues, covalent modifications and view confidence. Ping me if you encounter problems.

Both the input component and the molecule output component are individually reusable. Simply pip install gradio_cofoldinginput or gradio_molecule3d.