do we need to train a mAb/antigen pair to redesign the CDRs?
avilella opened this issue · comments
We have a few cases of mAb/antigen pairs where we know there is or isn't binding, but we don't know the exact binding mechanism (epitope/paratope).
If we want to increase binding or stability of a mAb/antigen pair with RefineGNN, starting with an Alphafold multimer pdb of the mAb Fv and the antigen (which may be wrong), how do we run RefineGNN to redesign the CDRs to increase the affinity/binding?
Do we need to train our mAb/antigen pairs to redesign the CDRs?