Methods of selecting binding reagents

A method for characterizing an affinity reagent which binds a desired peptide epitope in a plurality of proteins, the method comprising:

• obtaining a peptide library comprising a variety of sequence contexts, each peptide of the peptide library comprising the sequence αXβ, wherein X is the desired peptide epitope, wherein X is a sequence of two to seven amino acids, wherein each of α and β comprises at least one amino acid, and wherein each of α and β varies amongst the variety of sequence contexts within the peptide library;
• screening a library of different affinity reagents against the peptide library to obtain the affinity reagent from the library of different affinity reagents which binds the desired peptide epitope X in at least 10% of the variety of the sequence contexts;
• obtaining binding measurements between the affinity reagent from the library of affinity reagents and a plurality of known protein sequences;
• and
• based upon the binding measurements of the affinity reagent from the library of affinity reagents to the plurality of known protein sequences, determining a model for the affinity reagent, wherein the model infers a binding probability of the affinity reagent from the library of affinity reagents to any protein given a sequence of the protein.