More info via this link or via DM

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

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

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:

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.

We've made available a ChimeraX extension and a Webapp to easily run predictions. AllMetal3D is now also easily installable using pip. ChimeraX: https://t.co/92fqLB8fUV HuggingFace: https://t.co/w7uymlxbqg Docs for Python Package: https://t.co/ixFBQt0LlS

Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions https://t.co/miPMphfhC9

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 😄) https://t.co/J2eN8q4w6f

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:

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).

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.

This is a portable interface. You can easily run in on your local infrastructure using Docker. There is also a REST API interface.

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: https://t.co/yvnZCKUQiU

All platforms that forbid commercial use like BioRender or BioGDP are simply incompatible with Open Access publishing under CC BY even if they claim otherwise. Your CC BY published paper will likely need a correction in the future to fix the copyright if you use e.g BioRender.

This is a great effort by NIH. All illustrations financed by public money should similarly be available for others to reuse in the correct format (vector). The key is that NIH BioArt is not only free but also comes with a permissive license! #OpenScience

You can play with the demos directly in the slides thanks to @Slidevjs 😎

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:

And if you want to support BioIcons in funding applications and make your voice heard it is still appreciated if you fill the user survey and tell us what you need from open scientific icons: