In
design binders via RFdiffusion and ProteinMPNN-FastRelax, at the beginning of
sequence design and binder assessment script mpnn_af.slm, we could perform a fitering step to remove useless backnones.
In my opinion, this is a very heloful step, because it greatly increase the speed and efficiency of desigining reasonable binders. For example, in my target.pdb, I only expect designed binders could bind with the outside part of the target.pdb (see fig.1).
fig.1 target.pdb and atoms where binders should bind with
fig.2 distribution of all designed backbone centers