Adding support for interactive MSA viewing, including coloring by entropy! Auto download from AFDB (for both uniprot and pdb entries). (4/4)

Save vectorized SVG for infinitely ♾ zoomable figures. (including support for contacts).

See example:
biorxiv.org/content/10.1...

Zhidian Zhang @yoakiyama.bsky.social @yehlincho.bsky.social @jajoosam.bsky.social

(3/4)

Adding record button to save animation. (2/4)

Maybe something akin to paper2agent:
huggingface.co/papers/2509....

hmmm... any ideas why mpnn would make things worse for af2, but make things about the same as af2 when used with boltz?

Yeah, we would expect the pseudo-likelihood to be maximized for best paired MSA!

We'll add an option to add custom MSA inputs to the notebook (later tonight). 😎

It was expected. The surprising part for me was that AlphaFold doesn't seem to care....

See study here from @lindseyguan.bsky.social
www.biorxiv.org/content/10.1...

This makes me wonder if the reason it doesn't seem to care is because it was trained on and evaluated on poorly paired MSAs. 🤔

2Y69 is technically "prokaryotic" as it's from the mitochondria. 🧐

We find this to be true across a number of targets. Where method used to pair sequences and filter them makes a big difference. This we find to be important when trying to disentangle paralogs from orthologs (4/4).