Computational Approaches for Studying Enzyme Mechanism Part A

Department of Chemistry, University of Chicago, USA

• 1. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme CatalysisYue Yang, Lili Pan, Felice C. Lightstone and Kenneth M. Merz, Jr.2. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in ProteinsAkshaya Kumar Das and Markus Meuwly3. Generalized Ensemble Sampling of Enzyme Reaction Free Energy PathwaysDongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng and Wei Yang4. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis Fiona L. Kearns, Phillip S. Hudson, Stefan Boresch and H. Lee Woodcock5. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme ReactionsYanzi Zhou, Shenglong Wang, Yongle Li and Yingkai Zhang6. QM/MM Calculations on ProteinsUlf Ryde 7. 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 Rovira8. Towards Determining ATPase Mechanism in ABC-Transporters: Development of the Reaction Path Force Matching QM/MM MethodYan Zhou, Pedro Ojeda-May, Mulpuri Nagaraju and Jingzhi Pu9. QM/MM Analysis of Transition States and Transition State Analogues in MetalloenzymesDaniel Roston and Qiang Cui10. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme ReactionsMudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan and Dan Thomas Major11. Examinations of the Chemical Step in Enzyme CatalysisPriyanka Singh, Zahidul Islam and Amnon Kohen 12. Use of QM/DMD as a Multiscale Approach to Modelling Metalloenzymes Nathan M. Gallup and Anastassia N. Alexandrova13. Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent ExchangeAdam Duster, Christina Garza and Hai Lin14. Enzymatic Kinetic Isotope Effects from Path Integral  Free Energy Perturbation  (PI- FEP) TheoryJiali Gao15. Simulating Nuclear and Electronic Quantum Effects in EnzymesLu Wang, Christine M. Isborn and Thomas E. Markland16. Using Molecular Simulation to Study Biocatalysis in Ionic LiquidsK. G. Sprenger and  Jim Pfaendtner17. The MoD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-QuadruplexesMikhail Askerka, Junming Ho, Enrique R. Batista, Jose A Gascón and Victor S. Batista

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