Computational Approaches for Studying Enzyme Mechanism Part B

Department of Chemistry, University of Chicago, USA

1. 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.
2. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins
Akshaya Kumar Das and Markus Meuwly
3. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways
Dongsheng Wu, Mikolai I. Fajer, Liaoran Cao, Xiaolin Cheng and Wei Yang
4. 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
5. Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions
Yanzi Zhou, Shenglong Wang, Yongle Li and Yingkai Zhang
6. QM/MM Calculations on Proteins
Ulf 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 Rovira
8. Towards 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
9. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes
Daniel Roston and Qiang Cui
10. Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions
Mudit Dixit, Susanta Das, Anil Ranu Mhashal, Reuven Eitan and Dan Thomas Major
11. Examinations of the Chemical Step in Enzyme Catalysis
Priyanka Singh, Zahidul Islam and Amnon Kohen
12. Use of QM/DMD as a Multiscale Approach to Modelling Metalloenzymes
Nathan M. Gallup and Anastassia N. Alexandrova
13. Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange
Adam Duster, Christina Garza and Hai Lin
14. Enzymatic Kinetic Isotope Effects from Path Integral  Free Energy Perturbation  (PI- FEP) Theory
Jiali Gao
15. Simulating Nuclear and Electronic Quantum Effects in Enzymes
Lu Wang, Christine M. Isborn and Thomas E. Markland
16. Using Molecular Simulation to Study Biocatalysis in Ionic Liquids
K. G. Sprenger and  Jim Pfaendtner
17. 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