Journal
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
Volume 17, Issue 15, Pages 4258-4261Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.bmcl.2007.05.038
Keywords
ligand efficiency; fragment based design; binding affinity
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Ligand efficiency is a simple metric for assessing whether a ligand derives its potency from optimal fit with the protein target or simply by virtue of making many contacts. Comparison of protein-ligand binding affinities for over 8000 ligands with 28 protein targets shows conclusively that the average ligand binding affinities are not linear with molecular size. It is therefore important to scale ligand efficiencies by the size of the ligand, particularly where small ligands (e.g., fragments) are involved. We propose a simple 'fit quality' metric that removes this dependence. (c) 2007 Elsevier Ltd. All rights reserved.
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