this is a conceptual question.
The protein I am working with has 2 domains (2 chains), and I would like to redesign part of the surface of each domain AND the interface between those domains.
I see two possibilities here (maybe there are more):
Option #1- Break the design into three smaller problems - i.e., design only chain A, then design only chain B, and finally, design the interface (5 residues + 7 residues + 11 residues).
Option #2- Design all residues at the same time (23 residues).
I am planning to redesign the residues and restrict repacking to only the neighbor residues; I wonder what is the best tradeoff between search space, computing time and accurate conformations.
Can you please advise on that?
Thanks in advance.