Protein-protein interactions represent a large and important group of drug targets involved in the development and progression of human diseases. However, their utilization in drug discovery has been hampered by the low probability of identifying small-molecule inhibitors able to disrupt protein binding with desirable potency and selectivity. Therefore, the capability for rapid screening of large compound libraries has been critical for the exploration of this target class. The present invention relates to a homogeneous time-resolved fluorescence assay for identification of inhibitors of Cks1-Skp2 binding that plays a critical role in the ubiquitin-dependent degradation of p27. The assay was implemented in a 1536-well format using the new Zeiss uHTS robot and achieved a throughput in excess of 100,000 data points per day. A protocol for a fully automated high throughput IC.sub.50 determination was developed for hit validation. The basic 1536 well screening platform reported here is simple, robust and cost effective. It is widely applicable to any protein-protein interaction of therapeutic interest.