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Among other tasks, it is necessary to analyze huge databases of small molecules. Since a direct relationship between the structure of these molecules and their effect (e.g., toxicity) can be assumed in many cases, a wide set of methods is based on the modeling of the molecules as graphs with attributes.<\/jats:p><jats:p>Here, we discuss our results concerning <jats:italic>structural<\/jats:italic> molecular similarity searches and molecular clustering and put them into the wider context of graph similarity search. 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