Journal
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
Volume 1754, Issue 1-2, Pages 221-224Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.bbapap.2005.07.041
Keywords
structure-based drug discovery; computer-aided drug design; induced fit; molecular dynamic; computer simulation; free energy
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induced-fit effects are well known in the binding of small molecules to proteins and other macromolecular targets. Among other targets, protein kinases are particularly flexible proteins, so that such effects should be considered in attempts at structure-based inhibitor design for kinase targets. This paper outlines some recent progress in methods for including target flexibility in computational studies of molecular recognition. A focus is the relaxed complex method, in which ligands are docked to an ensemble of conformations of the target, and the best complexes are re-scored to provide predictions of optimal binding geometries. Early applications of this method have suggested a new approach to the development of inhibitors of HIV-1 Integrase. (c) 2005 Elsevier B.V All rights reserved.
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