title: Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.
abstract: Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this minipresentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study.
authors: Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States.
authors: D
authors: D
authors: Wu
authors: UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Florida State University, Tallahassee, FL, United States.
authors: M I
authors: MI
authors: Fajer
authors: Florida State University, Tallahassee, FL, United States.
authors: L
authors: L
authors: Cao
authors: UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; The University of Tennessee, Knoxville, TN, United States. Electronic address: chengx@ornl.gov.
authors: X
authors: X
authors: Cheng
authors: Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States; Florida State University, Tallahassee, FL, United States. Electronic address: yyang2@fsu.edu.
authors: W
authors: W
authors: Yang
mesh_terms: D000465:Algorithms; D000818:Animals; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D004798:Enzymes
keywords: Enzyme reaction; Generalized ensemble sampling; Minimum free energy path