The notion of molecular similarity (or chemical similarity) is one of the most important concepts in chemoinformatics. It plays an important role in modern approaches to predicting the properties o chemical compounds, designing chemicals with a predefined set of properties and, especially, in conducting drug design studies by screening large databases containing structures of available (or potentially available) chemicals. These studies are based on the similar property principle of Johnson and Maggiora, which states: similar compounds have similar properties.

Molecular similarity in virtual screening

The similarity-based virtual screening assumes that all compounds in a database that are similar to a query compound have similar biological activity. Although this hypothesis is not always valid, quite often the set of retrieved compounds is considerably enriched with actives.