Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org

🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters

Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8)

Preprint: www.biorxiv.org/content/10.1...

(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)

[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

Who knew a Nobel Prize win could unlock an entire city? Join us live on YouTube as we celebrate 2024 Nobel Laureate David Baker together with the Mayor of Seattle and many others on March 10th starting at 5 pm (PT)! 🥇🔑🌇

www.youtube.com/live/z8NO4Bg...

A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.

I use it a lot for my protein design workflows together with @biotite.bsky.social.

Just `pip install pymol-remote`

#CompChemSky 🧶🖥️🧬🧪
I wonder, is there any computational approach, that would find protein in PDB according to any arbitrary shape?

The Praetorius lab for Biomolecular Design at the Institute of Science and Technology Austria (ISTA) is looking for grad students in 2024. If you are interested in protein design at a great institute near Vienna reach out to me!
www.dropbox.com/scl/fi/6iny2...

Update on the Chroma vs RfDiffusion analysis.

ProteinMPNN just doesn't like Chroma's backbones (poor prediction of proteinMPNN generated sequences by ESMFold). Interestingly, Chroma's own sequence design method (which was trained in the context of partially noise backbones) loves it! (1/3)

"Performance and structural coverage of the
latest, in-development AlphaFold model" 🧪🧶🧬

DeepMind & Isomorphic Labs sharing some updates (but no code) on what is presumably alphafold 3, capable of modeling ligands, nucleic acids, antibody-antigen complexes etc

storage.googleapis.com/deepmind-med...