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Efficient 3D pharmacophore alignment as a tool for structure-based modeling and scoring

Chemical-feature based pharmacophore models have been established as state-of-the-art technique for bio-activity prediction. While in ligand-based drug design, chemical feature-based pharmacophore creation from a set of bio-active molecules is a frequently chosen approach, structure-based pharmacophores are still lacking the reputation to be an alternative or at least a supplement to docking techniques. Nevertheless, 3D pharmacophore screening bears the advantage of being much more efficient than unattended high-throughput docking and to transparently provide the user with all the information that is used by the screening algorithms to characterize the ligand-macromolecule interaction.

Our efficient, rigid 3D pharmacophore superpositioning technique [1] will be applied to a number of structure-based pharmacophores selected from a diverse set of targets. Molecule coordinates generated from geometric fitting of multi-conformational models of small organic molecules to structure-based pharmacophores are compared to docking poses and discussed in terms of scoring, conformational coverage, and eligibility for virtual screening.


  1. Wolber G, Dornhofer AA, Langer T: Efficient overlay of small organic molecules using 3D pharmacophores. J Comput Aided Mol Des. 2007, 20 (12): 773-788. 10.1007/s10822-006-9078-7.

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Correspondence to Gerhard Wolber.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Wolber, G. Efficient 3D pharmacophore alignment as a tool for structure-based modeling and scoring. Chemistry Central Journal 2 (Suppl 1), P49 (2008).

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