Depending on the type of restraint (actual residue-residue distances for example from NOE measurements vs. ambiguous from chemical shift or mutational data), your best bet may be Haddock

http://www.nmr.chem.uu.nl/haddock/

It deals with ambiguous restraints quite well.

There are several programme available for this purpose, some are free and some are not. You can use String for predict pp interaction with the action and evidence view.

@ Rene I know from experimental data which part of each protein is required for their interaction

Do you mean at the domain or residue level?

Dear Jeffrey, I meant at residues level. These residues are wel charactarized.

Depending on the type of restraint (actual residue-residue distances for example from NOE measurements vs. ambiguous from chemical shift or mutational data), your best bet may be Haddock

http://www.nmr.chem.uu.nl/haddock/

It deals with ambiguous restraints quite well.

Dear Jeffrey, Thanks for your support. It seems you have rather much knowledge/experience regarding such topics and requirements based on your answers and trackrecords. Any ideas on how to implement my question into a reasonable research question that could be publicable? Authorships are always negotiable.

I would have to know more about the particular protein you are studying and the information you have. You can contact me by email if you would like if you or your PI would like to keep this information confidential.

Dear Jeffrey, do you have a direct emailadress?

[email protected]

Dear Jeffrey, might it be possible to send you the pdb files including reported binding site residue sequence? The aim is to visualize/analyse the difference in binding between wt and mut protein and its normal ligand.