Computational Approaches for Studying Enzyme Mechanism Part A (Volume 577) (Methods in Enzymology, Volume 577)

Part A. The Role Of Molecular Dynamics Potential Of Mean Force Calculations In The Investigation Of Enzyme Catalysis / Yue Yang, Lili Pan, Felice C. Lightstone And Kenneth M. Merz, Jr. -- Empirical Force Fields For Mechanistic Studies Of Chemical Reactions In Proteins / Akshaya Kumar Das And Markus Meuwly -- Generalized Ensemble Sampling Of Enzyme Reaction Free Energy Pathways / Dongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng And Wei Yang -- Methods For Efficiently And Accurately Computing Quantum Mechanical Free Energies For Enzyme Catalysis / Fiona L. Kearns, Phillip S. Hudson, Stefan Boresch And H. Lee Woodcock -- Born-oppenheimer Ab Initio Qm/mm Molecular Dynamics Simulations Of Enzyme Reactions / Yanzi Zhou, Shenglong Wang, Yongle Li And Yingkai Zhang -- Qm/mm Calculations On Proteins / Ulf Ryde --^ Enzymatic Cleavage Of Glycosidic Bonds: Strategies On How To Setup And Control A Qm/mm Metadynamics Simulation / Lluís Raich, Alba Nin-hill, Albert Ardèvol And Carme Rovira -- Toward Determining Atpase Mechanism In Abc-transporters: Development Of The Reaction Path Force Matching Qm/mm Method / Yan Zhou, Pedro Ojeda-may, Mulpuri Nagaraju And Jingzhi Pu -- Qm/mm Analysis Of Transition States And Transition State Analogues In Metalloenzymes / Daniel Roston And Qiang Cui -- Practical Aspects Of Multiscale Classical And Quantum Simulations Of Enzyme Reactions / Mudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan And Dan Thomas Major -- Examinations Of The Chemical Step In Enzyme Catalysis / Priyanka Singh, Zahidul Islam And Amnon Kohen -- Use Of Qm/dmd As A Multiscale Approach To Modelling Metalloenzymes / Nathan M. Gallup And Anastassia N. Alexandrova --^ Adaptive Partitioning Qm/mm Dynamics Simulations For Substrate Uptake, Product Release, And Solvent Exchange / Adam Duster, Christina Garza And Hai Lin -- Enzymatic Kinetic Isotope Effects From Path-integral Free Energy Perturbation Theory / Jiali Gao -- Simulating Nuclear And Electronic Quantum Effects In Enzymes / Lu Wang, Christine M. Isborn And Thomas E. Markland -- Using Molecular Simulation To Study Biocatalysis In Ionic Liquids / K. G. Sprenger And Jim Pfaendtner -- The Mod-qm/mm Method: Applications To Studies Of Photosystem Ii And Dna G-quadruplexes / Mikhail Askerka, Junming Ho, Enrique R. Batista, Jose A Gascón And Victor S. Batista. Part B. Continuum Electrostatics Approaches To Calculating Pkas And Ems In Proteins / M.r. Gunner, N.a. Baker -- Path Sampling Methods For Enzymatic Quantum Particle Transfer Reactions / M.w. Dzierlenga, M.j. Varga, S.d. Schwartz -- Accurate Calculation Of Electric Fields Inside Enzymes / X. Wang, X. He, J.z.h. Zhang -- Molecular Dynamics Studies Of Proton Transport In Hydrogenase And Hydrogenase Mimics / B. Ginovska, S. Raugei, W.j. Shaw -- Modeling Mercury In Proteins / J.m. Parks, J.c. Smith -- Steered Molecular Dynamics Methods Applied To Enzyme Mechanism And Energetics / C.l. Ramírez, M.a. Martí, A.e. Roitberg -- New Algorithms For Global Optimization And Reaction Path Determination / D. Weber, D. Bellinger, B. Engels -- Simulation Studies Of Protein And Small Molecule Interactions And Reaction / L. Yang, J. Zhang, X. Che, Y.q. Gao -- How To Run Fast Simulations / M.i. Zimmerman, G.r. Bowman --^ Bridging Enzymatic Structure Function Via Mechanics: A Coarse-grain Approach / S. Sacquin-mora -- A Networks Approach To Modeling Enzymatic Reactions / P. Imhof -- Conformational Sub-states And Populations In Enzyme Catalysis / P.k. Agarwal, N. Doucet, C. Chennubhotla, A. Ramanathan, C. Narayanan -- Computation Of Rate Constants For Diffusion Of Small Ligands To And From Buried Protein Active Sites / P.-h. Wang, D. De Sancho, R.b. Best, J. Blumberger -- Calculation Of Enzyme Fluctuograms From All-atom Molecular Dynamics Simulation / T.h. Click, N. Raj, J.-w. Chu -- Constructing Kinetic Network Models To Elucidate Mechanisms Of Functional Conformational Changes Of Enzymes And Their Recognition With Ligands / L. Zhang, H. Jiang, F.k. Sheong, F. Pardo-avila, P.p.-h. Cheung, X. Huang --^ Microscopic Characterization Of Membrane Transporter Function By In Silico Modeling And Simulation / 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 -- Detecting Allosteric Networks Using Molecular Dynamics Simulation / S. Bowerman, J. Wereszczynski. Edited By Gregory A. Voth. Includes Bibliographical References And Indexes.