Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 71, Issue -, Pages 233-241Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2016.11.018
Keywords
Binding free energy; Alchemical simulations; Solute tempering; Hamiltonian Replica Exchange; Jarzynski theorem; Crooks theorem; Drug-receptor; Molecular dynamics; Nonequilibrium process
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Alchemical molecular dynamics simulations for evaluating the binding free energy in ligand-receptor systems are emerging a new powerful tool for in silica drug discovery projects. Nonetheless, theoretical and technical challenges for these methodologies remain high and their use in industrial applications is still limited. In this contribution, the many variants of the alchemical approach are critically revised, discussing their strengths as well as their pitfalls and entanglements and placing existing computational theories into the broader context of nonequilibrium thermodynamics. (C) 2016 Elsevier Inc. All rights reserved.
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