Using motif scaffolds for binder design

[egrabovac]

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!

[ardhe-qb]

Hi,

I would also be very interested in the above. Have you by any chance received any updates on this topic @egrabovac ?

Thanks!