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

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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.

References

  1. 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 (https://creativecommons.org/licenses/by/2.0), 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, P49 (2008) doi:10.1186/1752-153X-2-S1-P49

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Keywords

  • Virtual Screening
  • Pharmacophore Model
  • Conformational Coverage
  • Screen Algorithm
  • Docking Technique