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Open Access Highly Accessed Review

Molecular dynamics simulations and drug discovery

Jacob D Durrant1* and J Andrew McCammon234

Author Affiliations

1 Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA

2 Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093, USA

3 Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA

4 Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA

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BMC Biology 2011, 9:71  doi:10.1186/1741-7007-9-71

Published: 28 October 2011

Abstract

This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. The limitations of current simulation methodologies, including the high computational costs and approximations of molecular forces required, are also discussed. With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role.

Keywords:
molecular dynamics simulations; computer-aided drug discovery; cryptic binding sites; allosteric binding sites; virtual screening, free-energy prediction