1. use ProteinMPNN to make variants of Ephrin B-2, a known binder/substrate 2. then manually fixing the binding site of the generated protein to an appropriate binding site in order to ensure that the residues at the docking site are also c…
Description
use ProteinMPNN to make variants of Ephrin B-2, a known binder/substrate
then manually fixing the binding site of the generated protein to an appropriate binding site in order to ensure that the residues at the docking site are also compatible (since ProteinMPNN only ensures the backbone shape is invariant)
iterative testing using AlphaFold to discover amino acid variations that appear to be beneficial for binding (using ipTM + ipSAE) and then select/test proteins with these variations