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J Comput Chem. 2008 Jan 15;29(1):108-14.

Shapelets: possibilities and limitations of shape-based virtual screening.

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Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323, Frankfurt am Main, Germany.


Complementarity of molecular surfaces is crucial for molecular recognition. A method for representation of molecular shape is presented. We decompose the molecular surface into commensurate patches with defined shape by fitting hyperbolical paraboloids onto a triangulated isosurface of the Gaussian model of a molecule. As a result of this decomposition we obtain a 3D graph representation of the molecular shape, which can be used for complete and partial shape matching and isosteric group searching. To point out the possibilities and limitations of shape-only models, we challenged our method by three scenarios in a virtual screening contest: rigid body alignment, consensus shape filtering, and target-specific screening.


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