A molecular equivalence number (meqnum) classifies a molecule with respect to a class of structural features or topological shapes such as its cyclic system or its set of functional groups. Meqnums can be used to organize molecular structures into nonoverlapping, yet highly relatable classes. We illustrate the construction of some different types of meqnums and present via examples some methods of comparing diverse chemical libraries based on meqnums. In the examples we compare a library which is a random sample from the MDL Drug Data Report (MDDR) with a library which is a random sample from the Available Chemical Directory (ACD). In our analyses, we discover some interesting features of the topological shape of a molecule and its set of functional groups that are strongly linked with compounds occurring in the MDDR but not in the ACD. We also illustrate the utility of molecular equivalence indices in delineating the structural domain over which an SAR conclusion is valid.
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