Using motif scaffolds for binder design

Hello,

Thanks so much for making this work available on Github!

I am trying to design a binder by using RF diffusion to generate the CDR regions of a pre-exisiting nanobody.

When using motif scaffolding to design binders, the motif and target are fixed in the positions/orientations they have in the input pdb. However, I want to give the designed nanobody the freedom to chose where it binds. I have tried using the fold conditioning methods discussed, but they also modify the portions of the scaffold protein that I wish to remain constant.

Any suggestions on how to design binders that use motifs without fixing their position relative to the target?

Thanks!

The issue does not name any files, tests, or entry points. Start by reviewing the existing motif scaffolding and fold conditioning methods, then determine whether the requested unconstrained motif placement is supported; done would be a documented approach or a clearly scoped implementation plan.