Computational Approaches for Studying Enzyme Mechanism Part B, Volume 578

Content: 
Series Page Page ii  
Copyright Page iv  
Contributors Pages xi-xiv  
Preface Pages xv-xvi G.A. Voth 
Chapter One - The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis Pages 1-29 Y. Yang, L. Pan, F.C. Lightstone, K.M. Merz Jr. 
Chapter Two - Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins Pages 31-55 A.K. Das, M. Meuwly 
Chapter Three - Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways Pages 57-74 D. Wu, M.I. Fajer, L. Cao, X. Cheng, W. Yang 
Chapter Four - Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis Pages 75-104 F.L. Kearns, P.S. Hudson, S. Boresch, H.L. Woodcock 
Chapter Five - Born–Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions Pages 105-118 Y. Zhou, S. Wang, Y. Li, Y. Zhang 
Chapter Six - QM/MM Calculations on Proteins Pages 119-158 U. Ryde 
Chapter Seven - Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation Pages 159-183 L. Raich, A. Nin-Hill, A. Ardèvol, C. Rovira 
Chapter Eight - Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path–Force Matching QM/MM Method Pages 185-212 Y. Zhou, P. Ojeda-May, M. Nagaraju, J. Pu 
Chapter Nine - QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes Pages 213-250 D. Roston, Q. Cui 
Chapter Ten - Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions Pages 251-286 M. Dixit, S. Das, A.R. Mhashal, R. Eitan, D.T. Major 
Chapter Eleven - Examinations of the Chemical Step in Enzyme Catalysis Pages 287-318 P. Singh, Z. Islam, A. Kohen 
Chapter Twelve - Use of QM/DMD as a Multiscale Approach to Modeling Metalloenzymes Pages 319-339 N.M. Gallup, A.N. Alexandrova 
Chapter Thirteen - Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange Pages 341-357 A. Duster, C. Garza, H. Lin 
Chapter Fourteen - Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory Pages 359-388 J. Gao 
Chapter Fifteen - Simulating Nuclear and Electronic Quantum Effects in Enzymes Pages 389-418 L. Wang, C.M. Isborn, T.E. Markland 
Chapter Sixteen - Using Molecular Simulation to Study Biocatalysis in Ionic Liquids Pages 419-441 K.G. Sprenger, J. Pfaendtner 
Chapter Seventeen - The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes Pages 443-481 M. Askerka, J. Ho, E.R. Batista, J.A. Gascón, V.S. Batista 
Author Index Pages 483-511  
Subject Index Pages 513-522