Ab initio protein-protein docking

HADDOCK
1

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

2

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

3

Hi,
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/

4

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.

5

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