I can't believe peptide inhibition is a valid epitope mapping method - (Feb/12/2016 )

I'm looking at section 6.2 of GE's Biacore Assay Handbook. Apparently if you have a peptide that is... what would the word be... orthologous? Homologous? to a section of a protein antigen, you can test if that peptide inhibits analyte binding to the antigen. I would've thought tertiary structure factors would preclude this as a possibility? A peptide homologous to a section of a protein I would think is drastically different from that section of protein because the peptide doesn't have any secondary or tertiary structure, while the protein does and is therefore different structurally?

Not necessarily... epitopes are usually 8 aa or less long (sometimes as short as 4 aa) and can even be specific for things like phosphoryations. at these sizes secondary, but not tertiary structures come into play, other than that tertiary structure may prevent binding of an antibody to an internal portion of a protein... one of the reasons some Abs don't work on immunocyto-chemistry assays or IP but will work on a denaturing western.