Shapelets: Possibilities and limitations of shape-based virtual screening
Ewgenij Proschak
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Search for more papers by this authorMatthias Rupp
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Search for more papers by this authorSwetlana Derksen
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Search for more papers by this authorCorresponding Author
Gisbert Schneider
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, GermanySearch for more papers by this authorEwgenij Proschak
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Search for more papers by this authorMatthias Rupp
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Search for more papers by this authorSwetlana Derksen
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Search for more papers by this authorCorresponding Author
Gisbert Schneider
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, Germany
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323 Frankfurt am Main, GermanySearch for more papers by this authorAbstract
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. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
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