Ab initio protein-protein docking

Dear Haddock team

I am unable to find interaction data for the two proteins I am trying to dock. While I am fully aware that Haddock was not created for ab initio docking, I read through the Haddock-Capri run and tried to use what was applicable for my task. Since I am using the web-based version I cannot continue unless i define active and passive residues, which I do not know for my proteins. Is there a possible workaround or a way to continue without defining interacting residues, even if the proteins are not similar or symmetrical?

Thank you in advance for your answer and your time

You can do that using center of mass restraints, but you will need to request Guru access. If you are not sure how to request that, have a look at this other thread: Guru and Expert privileges

if you do not have any information about the interface you can also define all surface residues as passive ((https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/)) or define randomly ambiguous interaction restraints from accessible residues (https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/) . HADDOCK then offers you the possibility to change the relative solvent accessibility cutoff. More info about restraints definition in our best practice guide: https://www.bonvinlab.org/software/bpg/restraints/

Thank you for the fast replies and your help.
I guess I was confused by how to define random AIRs.
I could proceed by defining the full length of both molecules as semi-flexible and then activating random patches in the docking parameter tab.

Let HADDOCK deals with the flexibly using the default automatic mode.