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Automatic atom mapping attempts to determine the correspondence between the atoms of the reactants and products of a chemical reaction. Such mappings are useful for allowing greater specificity in queries of reaction databases. Recently there has been increased interest in their use to assist in the validation and standardisation of reactions in pharmaceutical ELNs (electronic lab notebooks). Atom mappings can, for example, detect if a reactant is missing or if a reactant does not contribute atoms to the product and hence may be better stored as an agent.
We have evaluated the performance of the new atom mapping algorithm introduced with Marvin v6 compared to the prior version on a publically available dataset extracted from the patent literature and on reactions from multiple pharmaceutical ELNs. Dramatic improvements are observed in all cases both in the percentage of reactions that can be successfully atom-mapped and the quality of mappings produced.
Finally we examine the difficulties that remain in validating reactions for which a complete atom mapping is not possible, such as for “routine” reactions where the reactant that was added is missing.