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Putting molecular similarity into context: asymmetric indices for field-based similarity measures


Some of the most widely used indices in molecular similarity searching are intrinsically symmetric in nature, meaning that each molecule under comparison contributes equally to the similarity index. For example, the Carbó and the Hodgkin–Richards similarity indices are respectively, related to the geometric and arithmetic averages of the molecular self-similarities. This work introduces the asymmetric forms of an entire family of field-based molecular similarity indices. By incorporating a weighted contribution of each molecule into the similarity index, the newly obtained asymmetric forms allow for measuring and modulating the similarity of one molecule in the context of another and thus have the potential of alleviating the size dependency often observed in chemical similarity searching

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Correspondence to Jordi Mestres.

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Mestres, J., Maggiora, G.M. Putting molecular similarity into context: asymmetric indices for field-based similarity measures. J Math Chem 39, 107–118 (2006).

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  • asymmetric similarity
  • molecular fields
  • similarity searching
  • virtual screening