Chemical genomics projects generate enormous amounts of data in a relatively short period of time. A screening campaign against a single target can produce millions of data points before data refinement is performed [1]. Generated data must then be stored and crosslinked with data from other projects. Informatics plays a critical role in all high-throughput screening (HTS) campaigns because of the sheer volume of data that need to be interpreted and the speed at which data are generated.

Informatics activities during a screening campaign are traditionally split into two primary functions, screening informatics and cheminformatics [2–5], which are usually treated as two separate disciplines because of the different training and experience required. In brief, screening informatics concentrates efforts on data organization, quality control, accessibility, and visualization, whereas cheminformatics focuses on identification of dominant chemical structural scaffolds that demonstrate a biological advantage in an HTS campaign and recommendation of functional changes for structural optimization. Although there are stages during a screening campaign when screening informatics and cheminformatics work independently, for most of a campaign, close collaboration is required to provide the highest-quality information for decision-making processes. Both types of informatics utilize databases and specialized software to support experimental biologists and chemists. Importantly, the integration of chemical structure data with assay results must be maintained by both screening informatics and cheminformatics teams in order to be useful for future work. This chapter introduces basic applications of screening informatics and cheminformatics for HTS.