I am performing protein-protein docking with AtomPairConstaint (the experiment shows the distance between two ligands) and I have some questions:
a. Whether the ref2015 or ref2015_cst function considers the ligand (with params file)?
b. If I use ref2015_cst in the docking_protocol, does the score function consider the constraint weight in both low- and high-resolution stages?
c. Is the ref2015 function default weights suitable for scoring the docking structure as the scoring tutorial use docking weights?