Hello
I would like to perform protein-protein docking, and I do not have any experimental data showing how they are interacting and what is the binding interface of them. But, I used PesTo webserver and other online tools to identify the active residues for input in HADDOCK docking webserver. Now, I am in the 3rd step (Docking parameters). I just have a couple of questions. Do you recommend applying any restraints for my system (such as center-of-mass? I do not know which parameters should be True and marked for my aim?
Please guide me though that.
Dear Negin,
If you used PesTo to identify potential interacting residues, you should define them as active in the 2nd step, for each molecule, and make the automatic definition of neighbor residues as passive. Then in the 3rd step, forget about center-of-mass restraints, as the ones detected by PesTo (the active ones) will be used to drive the docking.
Cheers
And I’d suggest leaving another docking parameters as default. Since you’re dealing with protein-protein docking, default values should be suitable for this task