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Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment.

Hudson BD, Whitley DC, Ford MG, Swain M, Essex JW

Centre for Molecular Design, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2EG, UK, brian.hudson@port.ac.uk.

A pattern recognition algorithm for the alignment of drug-like molecules has been implemented. The method is based on the calculation of quantum mechanical derived local properties defined on a molecular surface. This approach has been shown to be very useful in attempting to derive generalized, non-atom based representations of molecular structure. The visualization of these surfaces is described together with details of the methodology developed for their use in molecular overlay and similarity calculations. In addition, this paper also introduces an additional local property, the local curvature (C (L)), which can be used together with the quantum mechanical properties to describe the local shape. The method is exemplified using some problems representing common tasks encountered in molecular similarity. Figure Molecular surfaces for Lorazepam (left) and Diazepam (right).

Published 26 November 2007 in J Mol Model.
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