Graph databases are becoming increasingly valued in the investigation of highly related datasets. One such example is matched-molecular pairs (MMPs), where the primary point of interest is often a transformation that relates similar structures to one another. This application study examines the use of ChemAxon’s proof-of-concept Neo4j Search Cartridge to represent and investigate MMP databases. Areas of focus include activity cliffs & activity pairs, chemically intelligent node searching and comparing transformations to provide context for activity values, as well as general investigation of the activity landscape.