An algorithm is described for comparing two sets of three-dimensional molecular coordinates to assess whether they correspond to the same conformer (within some small tolerance). The algorithm does not require or make use of connectivity information, and does not require a priori atomic correspondence information, though it will identify one or more viable atomic mappings if the two conformers are equivalent within the user-specified tolerance. In contrast to typical approaches (e.g. Kabsch algorithm) that make use of an RMSD metric, the algorithm uses an error metric based on maximum deviations between intraconformer atom-pair distances. The algorithm scales well with molecule size, avoiding the N! explosion of potential atomic mappings and achieving O(N2) scaling in the best case. Preliminary tests of the algorithm are described. The algorithm could be used in approaches to enumerate conformer ensembles, and is made available on the web through the open-source MoleCoor package.

Algorithm for efficient conformational equivalence testing without <i>a priori</i> atomic correspondence or connectivity information

245th National Meeting (2013)

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Algorithm for efficient conformational equivalence testing without a priori atomic correspondence or connectivity information