The present invention provides methods for identifying and/or rank ordering target polypeptides that interact with a candidate polypeptide. Potential targets for the candidate polypeptide are identified using an interaction assay. A set of mutants are derived from the candidate polypeptide and a functional profile is obtained for the set of mutants and the candidate polypeptide. Also, for each identified potential target, an interaction profile is obtained for the set of mutants and the candidate polypeptide. The interaction profiles are compared to the functional profile and based on the degree of correspondence between the profiles, the potential targets are identified and/or rank ordered as target polypeptides that interact to the candidate polypeptide.
