Molecular core structures (frameworks, scaffolds) and their biological activities have long been intensely studied in pharmaceutical research. Over the past ~15 years, formal definitions of molecular scaffolds have been introduced, from different perspectives, hence providing a general basis for scaffold analysis. A number of such analyses have been reported. For example, scaffold diversity among compounds from different sources has been assessed, scaffold topologies have been explored, and scaffold libraries have been created. Also, the study of scaffold-activity relationships has been increasingly refined, selected scaffolds have been associated with specific biological activities, and computational methods and structural organization schemes for activity prediction have been introduced. Moreover, in recent years, increasing emphasis has been put on data mining approaches to study scaffold-activity relationships on a large scale, catalyzed by the availability of large public domain repositories of compound activity data. Taken together, computational scaffold analyses of scaffolds extracted from bioactive compounds have provided a number of in part rather unexpected findings that also provide opportunities for future research.
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