Chemical similarity is a fundamental concept in cheminformatics and is used in various tasks, such as predicting biological activities or analyzing molecular datasets. A natural approach to quantifying the similarity of chemical compounds is based on the substructures they share. This chapter focuses on graph-based methods for comparing molecules, particularly algorithms for identifying the maximum common subgraph of two molecular graphs. We discuss the basic graph-theoretical formalizations and summarize the related computational problems, their theoretical complexity and the prevailing algorithmic techniques for their solution as well as corresponding applications.

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