Methods of preparing monoclonal antibodies that differentially bind to a single conformer of a protein of interest are described. Passive immunization using these antibodies as well as use of conformer-specific antibodies as diagnostic reagents for the purpose of stratification of patient populations with regards to disease outcome, drug efficacy or drug sensitivity is also disclosed as well as active immunization with the protein conformer. In the screening techniques, detection can be for example by tissue immunostaining, western blotting or solution IP. A specific mab termed 7VC which shows conformation specificity to CtmPrP, a prion protein conformer that triggers neurodegeneration under specific assay conditions of pH and copper concentration, is described. A second specific antibody termed 19B10 shows conformation specificity for NtmPrP, a prion protein conformer that downregulates total PrP expression and effects cell differentiation.