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, …)
But you can rescore the models in that way provided you write your own scoring function
Thanks, can I ask if this thought is reasonable?
My second thought is, the feature of HADDOCK is, it uses user-defined active/passive residues to guide the interaction. If the active residues are not penalised when not used, this unique feature will disappear, and makes HADDOCK similar to e.g.