I think missing annotations is the problem here. Until we have more complete sequenced proteomes, global phylogeny is likely to shift in the future

Huge congrats to lead authors Qiuzhen Li & Diandra Daumiller! Thanks to @martinsteinegger.bsky.social for all the great tools!
📄 Preprint: biorxiv.org/content/10.6...
🖥️ Try the Tool: she-app.serve.scilifelab.se

🕊️ Structural Acceleration
Does a bigger genome mean faster structural evolution? No.
We found lineage-specific bursts of structural innovation in Birds (Aves) and Ants (Hymenoptera) that are distinct from genomic expansion. (4/5)

⚙️ A Bipartite Evolutionary Mode
The eukaryotic proteome isn't a uniform soup.
We resolve it into two distinct modes:
A rigid "Architectural Core" (Cytoskeleton/Chaperones)
A highly plastic "Operational Engine" (Metabolism/Translation) (3/5)

🐁 Stop guessing your model organism.
Our new search engine allows you to rank model organisms by their structural fidelity to specific human pathways.
Case Study: For Fanconi Anaemia, Mouse is perfect. Yeast fails. C. elegans is a hidden gem. (2/5)

This is the first study from my lab - providing the first PoC for both linear and cyclic untargeted binder design! EvoBind is available here: github.com/patrickbryan...

We have much more coming in this space where we can identify target interfaces and inhibit the interactions - all using protein structure prediction!

The WT binder is 1.8 uM which means that we create as good binders but with new modes of binding for a target where these NCAA interactions are completely unknown 😎

Thanks! We will release a lot of new tech this year - stay tuned! We are only in the beginning of protein design I think

There is also an audio summary generated by Science Cast here: sciencecast.org/casts/4kj8lr...

Just like we have used EvoBind to e.g. create functional HIV inhibitors in a single shot (biorxiv.org/content/10.1...) we can now do this with an expanded vocabulary to have more chemical possibilities and avoid e.g. immune recognition and degradation

RareFold supports 49 different AAs.
The 20 regular, and 29 rare ones: MSE, TPO, MLY, CME, PTR, SEP,SAH, CSO, PCA, KCX, CAS, CSD, MLZ, OCS, ALY, CSS, CSX, HIC, HYP, YCM, YOF, M3L, PFF, CGU,FTR, LLP, CAF, CMH, MHO.
You can simply specify which you want to use and design!