How to perform blind docking of two proteins in HADDOCK?

Please let us know the steps to do blind protein protein docking in HADDOCK

HADDOCK has two ab-initio modes:

  1. Center of mass restraints: Defines a distance restraint between the center of masses of the proteins. Best for rather globular proteins

  2. Random patches: Randomly picks a solvent accessible residue on each protein and defines a patch around it. Ambiguous restraints are then generated between those two patches

Those options are available with advanced access to the server on the third submission tab (docking parameters).

In both cases, the sampling should be increased (e.g. 10000/400/400 for the three HADDOCK stages), and I would also recommend to put the minimum cluster size to 1 as there might not be much convergence.

You could also perform a statistical analysis of contacts and use the most contacted residues in a second targeted run (e.g. as described for small molecule docking in the following tutorial: https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/)

But remember HADDOCK was developed for integrative modelling and does best when information is provided to guide the docking.
For ab-initio docking there are other nice docking software to try, e.g. CLUSPRO, FRODOCK, LightDock, …