The application of chemical diversity in the discovery of novel drug molecules is a contentious issue.  The way in which chemical space is often defined - and thus sampled effectively - is by using the 2D connectivity maps of atoms within molecules. These maps can be encoded as numbered features which can be counted and compared.  Although this is a particularly effective method on a large scale it has deficiencies.  These largely spring from what fundamentally underpins the interaction of a molecule with its biological target, which is not related to the 2D chemical framework but to the 3D interaction of the surface of the molecule via shape and field complementarity.  We have investigated alternative methods of defining chemical space using 3D Field based methodologies - the advantages and disadvantages of which we will describe.

Assessing the similarity of compound collections using molecular fields: Does it add value?

243rd National Meeting (2012)

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