Hello,

I am running a sandwich-type ELISA where I am trying to inhibit a protein-protein interaction using small molecules. For each experiment, I determine my Z' (Z-prime) to determine the quality of the assay. To calculate the Z-prime, I use the mean and SD of positive and negative controls. My positive control (positive for signal) is both proteins in the absence of compound. Because there is no known small molecule inhibitor of this protein-protein, interaction, I simply remove one of the proteins and use that condition as my negative control (negative for signal). This gives a very good Z-prime, but my question is this: is it alright that I use a protein-devoid condition as my negative control for drug screening, or must I use a small molecule inhibitor to simulate chemical inhibition of the protein-protein interaction?

Thank you!