I’m a new HADDOCK user, and am trying to dock 2 proteins. I know residues involved in the binding interaction for one of the proteins, but I do not know binding residues for the other protein (stated differently, I know the binding interface for protein ‘A’, but I do not know where on protein ‘B’ protein ‘A’ binds). Intuitively, even this one-sided binding site information should help restrict docking and improve complex prediction. However, it appears that the HADDOCK web tool does not allow you to provide active site information for one protein but not the other. Is there any way to do this? Thanks!
Actually the web server does support this scenario, offering the option to define all solvent accessible residues are passive (but you might need higher level access to see that - simply request it in your registration page)
PS: You will also need to increase the sampling in this scenario (e.g. 10000/400 models)