Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
[HTML][HTML] The ONIOM method and its applications
The fields of theoretical and computational chemistry have come a long way since their
inception in the mid-20th century. Fifty years ago, only rudimentary approximations for very …
inception in the mid-20th century. Fifty years ago, only rudimentary approximations for very …
Modeling molecular interactions in water: From pairwise to many-body potential energy functions
Almost 50 years have passed from the first computer simulations of water, and a large
number of molecular models have been proposed since then to elucidate the unique …
number of molecular models have been proposed since then to elucidate the unique …
Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …
including the rearrangements of electrons in biochemical reactions, electron and proton …
Characterization of lipid–protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation
The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …
cell, where key processes such as selective transport of material and exchange of …
Computational electrochemistry: prediction of liquid-phase reduction potentials
This article reviews recent developments and applications in the area of computational
electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and …
electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and …
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” …
P450 Enzymes: Their Structure, Reactivity, and Selectivity Modeled by QM/MM Calculations
The introduction of oxygen into biochemical processes has brought about an evolutionary
leap in the history of life, whereby many organisms have evolved to use oxygen as part of …
leap in the history of life, whereby many organisms have evolved to use oxygen as part of …
Review on the QM/MM methodologies and their application to metalloproteins
The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was
introduced in 1976, while the extensive acceptance of this methodology started in the 1990s …
introduced in 1976, while the extensive acceptance of this methodology started in the 1990s …
Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins
Computational prediction of enzyme mechanism and protein function requires accurate
physics-based models and suitable sampling. We discuss recent advances in large-scale …
physics-based models and suitable sampling. We discuss recent advances in large-scale …