We describe Scaffold Hunter, an interactive software tool for the exploration and analysis of chemical compound databases. Scaffold Hunter allows to explore the chemical space spanned by a compound database, fosters intuitive recognition of complex structural and bioactivity relationships, and helps to identify interesting compound classes with a desired bioactivity. Thus, the tool supports chemists during the complex and time-consuming drug discovery process to gain additional knowledge and to focus on regions of interest, facilitating the search for promising drug candidates.

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