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Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding. A framework for combining multiple similarity computations is presented along with its systematic application to 358 drugs with overlapping pharmacology. Given a new molecule along with a set of molecules sharing some biological effect, a single score based on comparison to the known set is produced, reflecting either 2D similarity, 3Ddoi:10.1021/jm200666a pmid:21916467 pmcid:PMC3188662 fatcat:kdbe7yh4lfhpdcpv6wua3kizqa