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Molecular similarity is an important concept, and vital for rapid database searching and activities like clustering that are critical for day to day working by chemists. But what do we mean by similarity? It is rather subjective; for example, two molecules may have the same molecular weight, but be completely different – what is the correct measure and method to quantify this? The first paper describes traditional a priori and algebraic methods and the second is a cracking review of the concepts of similarity (see excellent diagram above as a taster).

Johnson, M.; Basak, S.; Maggiora, G. A characterization of molecular similarity methods for property prediction Mathematical and Computer Modelling, 1988, 11, 630-634

Maggiora, G.; Vogt, M.; Stumpfe, D.; Bajorath, J. Molecular Similarity in Medicinal Chemistry J. Med. Chem.2014, 57, 83186-3204

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