A new method has recently become available (Stigmata; Shemetulskis, et al., J. Chem. Inf. Comput Sci. (1996),36,862-871) for extracting the common element, termed the modal fingerprint, from a set of molecular fingerprints. Molecular fingerprints based on a topological description of the molecule capture atom and bond path information in binary form which is readily amenable to comparison. The modal fingerprints for a set of molecules, extracted at maximum, median or minimum strigencies, provide a profile of the degree of topological similarity (or dissimilarity) within a given collection of compounds. Approaches to using this tool to measure chemical diversity within and between chemical datasets and relating the derived metrics to qualitative chemical notions of diversity will be illustrated by considering data collections of various origins typical of those encountered by medicinal chemists. Some comparisons with other proposed 2D diversity measures will also be offered.

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