I hope this message finds you well. If I know two domains interact from yeast-two hybrid experiments, can I use the surface residues of the interacting domains to guide HADDOCK? Would I label all the surface residues from the two interacting domains as active residues? I am not sure if it is bad to have too many active residues with less precise data.
Using all surface residues as active is not a good idea…
Your domains might be part of a larger protein and some parts might not be accessible.
If you have no info, using center of mass restraints (ab initio mode) might be better.
You could also considering running our new Artic3D server on your two domains to see if some interfaces are already known:
Thank you for your helpful guidance.