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Bioorg Med Chem. 2008 Jan 1;16(1):422-7. Epub 2007 Sep 18.

The use of ligand-based de novo design for scaffold hopping and sidechain optimization: two case studies.

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Neurocrine Biosciences, 12790 El Camino Real, San Diego, CA 92130, USA.


This paper describes the application of de novo design utilizing exclusively ligand information. In the current approach, ligand design criteria, including pharmacophores, similarity and desired properties are applied as part of a fitness function driving the design process, instead of using them as filters after the process. This allows relevant parts of chemical space to be explored more efficiently. Two case studies of successful ligand design are also presented, one aimed at scaffold hopping, the other for exploring substitution patterns around a novel scaffold.

[Indexed for MEDLINE]

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