Single-motif scaffolding with scaffold as separate chain

[lindseyguan]

Thank you so much for your excellent work on this method!

I was wondering if there is currently a way to specify that I would like the generated scaffold to occupy its own chain. For example, if I wanted to design a length-20 peptide binder to 5WN9 chain A, is that supported?

REMARK 999 NAME   5WN9
REMARK 999 PDB    5WN9
REMARK 999 INPUT  A 1   250
REMARK 999 INPUT     20  20 # I would like this to be on a separate chain, like chain B or something
REMARK 999 MINIMUM TOTAL LENGTH      270
REMARK 999 MAXIMUM TOTAL LENGTH      270

[yeqinglin]

Thanks a lot and sorry for the late reply. Unfortunately, Genie 2 only supports monomer design (taking in a monomer as input) at the moment. However, extension to multimers and providing support for binder design is one of our active working direction.