title: Accelerated molecular dynamics in computational drug design.
abstract: The method of accelerated molecular dynamics (aMD) has been shown to increase the rate of phase-space sampling in biomolecular simulations. In this chapter, we discuss the theory behind aMD and describe the implementation of two versions: dual-boost and selective aMD. Each method has its practical advantages: dual-boost aMD is useful for increasing sampling of global conformational motions while selective aMD can improve the rate of convergence of free energy calculations. Special emphasis is placed on the use of these methods in computer-aided drug design, and the example of oseltamivir binding to neuraminidase is highlighted for both cases.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA. jmweresz@mccammon.ucsd.edu
authors.forename: Jeff
authors.initials: J
authors.lastname: Wereszczynski
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D006801:Humans; D056004:Molecular Dynamics Simulation; D009439:Neuraminidase / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D053139:Oseltamivir / Q000737:chemistry / Q000494:pharmacology; D013816:Thermodynamics
chemical_list: D053139:Oseltamivir; D009439:Neuraminidase