Enforcing a fold on designed binder

[arutik]

Hi,

I am trying to understand the design_ppi_scaffolded script. From the comments there, I gather that with this script I should be able to design a binder of a particular fold (let's say helical) - is that so? Because it looks like the adjacency matrix and secondary structure files provided in the input are for the target protein (not the binder to be designed), so I'm not sure how anything is enforced on the binder fold/conformation (unless there is a mistake in the comments for that script?).

Perhaps I am missing something, but in any case it would also be super useful if you are able to please provide the scaffolds (ppi_scaffolds) that are passed via scaffoldguided.scaffold_dir argument as I can't seem to find them anywhere in the repo.

Many thanks, Anna Arutyunyan

[overlord1647]

i think this is the file you want: ppi_scaffolds_subset.tar.gz. its in RFdiffusion/examples