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

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...

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...

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...

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

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.

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/

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...

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).