To compare chemical structures, we can look at a number of 2D and 3D characteristics. In this paper, a group of 358 drugs with overlapping pharmacology were assessed for chemical similarity, using a new framework.
The method generates a chemical similarity score for new molecules based on a known set of molecules with a shared effect. For prediction of primary targets, the benefit of 3D over 2D was relatively small, but for prediction of off-targets, the added benefit was large.
Emmanuel R. Yera et al., J. Med. Chem. 2011, 54, 19, 6771–6785.
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What are conformational ensembles? A conformational ensemble is a collection of the different 3D shapes a molecule can adopt in…
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