Computational Approaches for Studying Enzyme Mechanism Part A

1. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis<br>Yue Yang, Lili Pan, Felice C. Lightstone and Kenneth M. Merz, Jr.<br>2. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins<br>Akshaya Kumar Das and Markus Meuwly<br>3. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways<br>Dongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng and Wei Yang<br>4. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis <br>Fiona L. Kearns, Phillip S. Hudson, Stefan Boresch and H. Lee Woodcock<br>5. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions<br>Yanzi Zhou, Shenglong Wang, Yongle Li and Yingkai Zhang<br>6. QM/MM Calculations on Proteins<br>Ulf Ryde <br>7. Enzymatic Cleavage of Glycosidic Bonds: Strategies on how to Setup and Control a QM/MM Metadynamics Simulation <br>Lluís Raich,  Alba Nin-Hill, Albert Ardèvol and Carme Rovira<br>8. Towards Determining ATPase Mechanism in ABC-Transporters: Development of the Reaction Path Force Matching QM/MM Method<br>Yan Zhou, Pedro Ojeda-May, Mulpuri Nagaraju and Jingzhi Pu<br>9. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes<br>Daniel Roston and Qiang Cui<br>10. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions<br>Mudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan and Dan Thomas Major<br>11. Examinations of the Chemical Step in Enzyme Catalysis<br>Priyanka Singh, Zahidul Islam and Amnon Kohen <br>12. Use of QM/DMD as a Multiscale Approach to Modelling Metalloenzymes <br>Nathan M. Gallup and Anastassia N. Alexandrova<br>13. Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange<br>Adam Duster, Christina Garza and Hai Lin<br>14. Enzymatic Kinetic Isotope Effects from Path Integral  Free Energy Perturbation  (PI- FEP) Theory<br>Jiali Gao<br>15. Simulating Nuclear and Electronic Quantum Effects in Enzymes<br>Lu Wang, Christine M. Isborn and Thomas E. Markland<br>16. Using Molecular Simulation to Study Biocatalysis in Ionic Liquids<br>K. G. Sprenger and  Jim Pfaendtner<br>17. The MoD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes<br>Mikhail Askerka, Junming Ho, Enrique R. Batista, Jose A Gascón and Victor S. Batista