In drug discovery high-throughput screening, it is desirable to screen a drug target against a selection of chemicals that try to take advantage of as much of the appropriate chemical space as possible. The wider the chemical space that is sampled by the chemical library, the better the chance that high-throughput screening will find a "hit"—a chemical with an appropriate interaction in a biological model that might be developed into a drug. The chemical space of all possible chemical structures is extraordinarily large. To balance the cost of screening many hundreds of thousands of inactive compounds in a large diverse compound library against the benefits such as directly establishing structure–activity relationships (SAR) from the screening data and increasing the chances of identifying a broad range of hit series, we designed two diversity sets: Mini Scaffold Library and Golden Scaffold Library. Selected from 1.6 million drug-like compounds with only 1 compound (Mini Scaffold Library, 5033 compounds) or 1-3 compounds (Golden Scaffold Library, 10000 compounds) for each scaffold, these two compound libraries can decrease the cost of screening and lower the screening threshold for single project team without compromise in losing sufficient information. In this case the initial screen will need to be followed by further rounds of purchase of compound analogues and screening to validate and expand the SAR around the hits.