Computational Approaches for Studying Enzyme Mechanism Part A

Content: 
Series Page Page ii  
Copyright Page iv  
Contributors Pages xi-xv  
Preface Pages xvii-xviii G.A. Voth 
Chapter One - Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins Pages 1-20 M.R. Gunner, N.A. Baker 
Chapter Two - Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions Pages 21-43 M.W. Dzierlenga, M.J. Varga, S.D. Schwartz 
Chapter Three - Accurate Calculation of Electric Fields Inside Enzymes Pages 45-72 X. Wang, X. He, J.Z.H. Zhang 
Chapter Four - Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics Pages 73-101 B. Ginovska, S. Raugei, W.J. Shaw 
Chapter Five - Modeling Mercury in Proteins Pages 103-122 J.M. Parks, J.C. Smith 
Chapter Six - Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics Pages 123-143 C.L. Ramírez, M.A. Martí, A.E. Roitberg 
Chapter Seven - New Algorithms for Global Optimization and Reaction Path Determination Pages 145-167 D. Weber, D. Bellinger, B. Engels 
Chapter Eight - Simulation Studies of Protein and Small Molecule Interactions and Reaction Pages 169-212 L. Yang, J. Zhang, X. Che, Y.Q. Gao 
Chapter Nine - How to Run FAST Simulations Pages 213-225 M.I. Zimmerman, G.R. Bowman 
Chapter Ten - Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach Pages 227-248 S. Sacquin-Mora 
Chapter Eleven - A Networks Approach to Modeling Enzymatic Reactions Pages 249-271 P. Imhof 
Chapter Twelve - Conformational Sub-states and Populations in Enzyme Catalysis Pages 273-297 P.K. Agarwal, N. Doucet, C. Chennubhotla, A. Ramanathan, C. Narayanan 
Chapter Thirteen - Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites Pages 299-326 P.-H. Wang, D. De Sancho, R.B. Best, J. Blumberger 
Chapter Fourteen - Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation Pages 327-342 T.H. Click, N. Raj, J.-W. Chu 
Chapter Fifteen - Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands Pages 343-371 L. Zhang, H. Jiang, F.K. Sheong, F. Pardo-Avila, P.P.-H. Cheung, X. Huang 
Chapter Sixteen - Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation Pages 373-428 J.V. Vermaas, N. Trebesch, C.G. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J.L. Baylon, T. Jiang, Y. Wang, M.P. Muller, E. Shinn, Z. Zhao, P.-C. Wen, E. Tajkhorshid 
Chapter Seventeen - Detecting Allosteric Networks Using Molecular Dynamics Simulation Pages 429-447 S. Bowerman, J. Wereszczynski 
Author Index Pages 449-477  
Subject Index Pages 479-494