QM/MM methods for biomolecular systems
HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
How enzymes work: analysis by modern rate theory and computer simulations
Advances in transition state theory and computer simulations are providing new insights into
the sources of enzyme catalysis. Both lowering of the activation free energy and changes in …
the sources of enzyme catalysis. Both lowering of the activation free energy and changes in …
Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology
Computational enzymology is a rapidly maturing field that is increasingly integral to
understanding mechanisms of enzyme-catalyzed reactions and their practical applications …
understanding mechanisms of enzyme-catalyzed reactions and their practical applications …
Quantum mechanical methods for enzyme kinetics
▪ Abstract This review discusses methods for the incorporation of quantum mechanical
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent …
W Wang, O Donini, CM Reyes… - Annual review of …, 2001 - annualreviews.org
▪ Abstract Computer modeling has been developed and widely applied in studying
molecules of biological interest. The force field is the cornerstone of computer simulations …
molecules of biological interest. The force field is the cornerstone of computer simulations …
Computer simulations of enzyme catalysis: methods, progress, and insights
A Warshel - Annual review of biophysics and biomolecular …, 2003 - annualreviews.org
▪ Abstract Understanding the action of enzymes on an atomistic level is one of the important
aims of modern biophysics. This review describes the state of the art in addressing this …
aims of modern biophysics. This review describes the state of the art in addressing this …
Mechanisms and free energies of enzymatic reactions
Most enzymatic reactions have very large and remarkably similar apparent second-order
rate constants, kcat/KM, at mean values of about 107 M-1 s-1 with kcat in the range of 10 …
rate constants, kcat/KM, at mean values of about 107 M-1 s-1 with kcat in the range of 10 …
Frontier bonds in QM/MM methods: A comparison of different approaches
A major complication in hybrid QM/MM methods is the treatment of the frontier between the
quantum part, describing the reactive region, and the classical part, describing the …
quantum part, describing the reactive region, and the classical part, describing the …
Energetics and dynamics of enzymatic reactions
J Villa, A Warshel - The Journal of Physical Chemistry B, 2001 - ACS Publications
This review considers the advances made in using computer simulations to elucidate the
catalytic power of enzymes. It is shown that some current approaches, and in particular the …
catalytic power of enzymes. It is shown that some current approaches, and in particular the …
Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation …
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used
to provide a general scheme for chemical reactions in proteins. However, such approaches …
to provide a general scheme for chemical reactions in proteins. However, such approaches …