CINF 111 |
| 3D pharmacophores have proven to be an efficient and comprehensive method to model ligand-macromolecule interactions describing both steric and chemical feature complementarity. In the context of the dense information content of a protein, the identification of pharmacophoric features is still complex: A promising way is combining automated feature generation with a comprehensive visual representation. In this work, a visualization framework that is capable of displaying the target molecule and the ligand together with its pharmacophore is presented. Two views are provided showing the receptor-ligand interactions, one in 3D and one in 2D. The pharmacophore features are generated automatically and can be visually verified by chemists by interacting with the display in the 3D view [1]. Additionally, the visualization of the binding pocket's surface provides essential information about the receptor-ligand interaction (e.g.: polarity of the surrounding environment). To overcome the inherent weaknesses of 3D representations, such as occlusion or the complexity of 3D perception, the framework provides a 2D view linked to the 3D representation of a particular ligand. This automatically calculated structure diagram displays the topology of the molecule, and also includes comprehensive visual metaphors for the pharmacophore features and associated amino acids. We present a convenient way of displaying pharmacophoric features in 3D as well as in 2D, suitable visual metaphors for pharmacophoric interactions, the generation of 2D layouts as collision-free as possible, and an implementation of linking and brushing among the views. [1] Wolber, G.; Kosara, R. Pharmacophores from macromolecular complexes with LigandScout. In 'Pharmacophores and Pharmacophore Searches', Langer, T.; Hoffmann, R., eds., Wiley-VCH: Weinheim, Germany, 2006; pp 131-150.
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General Papers
8:30 AM-11:25 AM, Thursday, 14 September 2006 Moscone Center -- Room 122, Oral
Division of Chemical Information |
