Chemoinformatics approaches to assess chemical diversity and complexity of small molecules

Abstract Small molecules have always been of interest in medicinal chemistry because of their ability to exert significant effects on the functions of macromolecules that comprise living systems. Chemical diversity and complexity are examples of properties to guide the design and selection of new small molecules. These properties may have significant implications in many areas of research including but not limited to drug and probe discovery. Systematic exploration of the chemical diversity and complexity of small molecules can be carried out using different strategies. A cornerstone in the different approaches is structure representation where the most common are molecular scaffolds, fingerprints, and whole molecule properties. This chapter discusses different cheminformatics strategies that have been consistently used in literature to characterize the diversity and complexity of small molecules. Recent exemplary studies of the diversity and complexity of small molecules and their interpretation are also discussed.