عنوان

Computational approaches for studying enzyme mechanism.

012805347X

9780128053478

dltt

Computational approaches for studying enzyme mechanism.

[Book]

edited by Gregory A. Voth

Part A /

xvi, 522 pages, 20] unnumbered pages of plates :

illustrations (some color) ;

24 cm

Methods in enzymology ;

volume 577

Includes bibliographical references and indexes

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

0

Enzymology

Voth, Gregory A.

20161018101223.0

rda

[Book]

Y