I would like to include all the CDR residues as active for the Fab. However, I do not want them to be penalised if they do not involve in interacting. Could this be possible?
My understanding for the algorithm is:
maximise the objective function
objective function = f_used(resi i, j, k, …) - f_unused(resi x, y, z, …)
Can I change it like this:
objective function = f_used(resi i, j, k, …)