Chemical similarity between two molecules is a fundamental concept in cheminformatics and structure comparison is therefore an often applied and important task. Structural comparison is used, e.g., to predict biological activities or to analyze molecular datasets. One approach for the identification of chemical similarity is based on a graph representation of molecules, because a molecule can intuitively be interpreted as a graph structure. In this article we focus on algorithms for the calculation of chemical similarity based on a graph representation, which is expressed as the maximum common substructure between two molecules.

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