Haddock model without knowing the binding interface

HADDOCK
1

Hello All,

For the protein complex (protein A-protein B), I know the residues of protein A involved in the interactions with protein B, but I have no clue of the binding area for protein B. Is it possible to apply haddock to get the complex structure model? If it is possible, how can I define the ambiguous distance restraints between protein A and protein B for the docking? Thank you very much!

2

You can try the following:

  1. Define the active residues on protein A (the ones involved in the interaction)

  2. Define the entire surface of protein B as passive (there is an option on the 2.4 web portal to do that automatically

  3. Increase the sampling to say 10000/400/400 models for the three stages of HADDOCK

3

Thanks a lot,

Bin