I am trying to dock molecules with the same parent core but different substitution groups into the same PDB structure using ROISE.
I tried to read through some published papers on ResettaLigand but still was not able to find out the answer for:
Since we are only allowed to include on ligand in each run, can we submit a few different runs and compare the interface score directly?
I am not sure about the algorism on whether the residue within a certain distances are consider or only interacting ones are considered. I guess in the latter case, we should not compare directly as different residues were used for scoring.
If someone could give a professional answer for this question, I would really appreciate your help.