Various assays have been employed to study the nuclear receptor/cofactor interactions. Coimmunopre-cipitation protocols, both yeast and mammalian two-hybrid systems, and electrophoretic mobility shift/ supershift assays are all commonly used. One of the most useful assays for studying direct protein—protein interactions is the glutathione-S -transferase “pulldown” assay. We have developed a high-throughput version of this assay that utilizes a filter microplate to allow parallel processing of many samples, significantly reducing the time and reagents required for the assay and increasing the sensitivity of the assay for weaker protein—protein interactions.