This invention provides, in one embodiment, a recombinant virus or a recombinant virus library wherein each virus comprises a protein involved in viral attachment or infection, a polypeptide which differs by at least a single amino acid from another peptide or polypeptide in the library, and a modified cleavage site that is proximal to the peptide and the protein, wherein the cleavage site is modified such that a compound mediating cleavage has a reduced binding affinity for it as compared to a non-modified cleavage site. The invention further provides a target of interest complex comprising a protease, a target of interest involved in an intermolecular interaction, and a flexible linker that attaches the protease and target of interest. The invention further provides uses thereof, including a method for identifying a peptide which has an intermolecular interaction with a target of interest or identifying the agonistic or antagonistic feature of a peptide that has an intermolecular reaction with a target of interest.