We present and discuss a new method that allows us to carry out very efficient flexible 3D substructure matching while at the same time deriving the conformers with the best atomic overlap with the query molecule. Given are a query molecule C, and a typically very large database delta containing information about a plurality of three-dimensional molecular structures each of which is able to exhibit torsional flexibility about one or more existing covalent bonds. Each of the molecules from the knowledge base is presented by a single conformer in the database; in fact, for the purposes of the method any which conformer suffices. The method determines those molecules from delta which contain substructures in common with substructures in the query molecule C in the presence of rotatable bonds. Additionally, the method determines the set of rigid transformations (i.e. rigid rotations and translations) that will put the pair (database and query molecules) in the best possible structural registration. Note that application of these computed transformations to the database molecule produces a novel conformer for the molecule; this derived conformer will in general be different from the conformer that was entered in the database, and no sampling of the respective molecules conformational space is required at any time during execution. The method make efficient use of lookup tables, thus effectively trading space for computation and exhibits superb scalability characteristics.
By: Isidore Rigoutsos, Daniel Platt and Andrea Califano
Published in: RC20497 in 1996
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