Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states

E Brunk, U Rothlisberger - Chemical reviews, 2015 - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …

Action of molecular switches in GPCRs-theoretical and experimental studies

B Trzaskowski, D Latek, S Yuan… - Current medicinal …, 2012 - ingentaconnect.com
G protein coupled receptors (GPCRs), also called 7TM receptors, form a huge superfamily of
membrane proteins that, upon activation by extracellular agonists, pass the signal to the cell …

Cis− trans isomerization of organic molecules and biomolecules: implications and applications

C Dugave, L Demange - Chemical reviews, 2003 - ACS Publications
Organic molecules as well as metal complexes may exist as several geometric isomers1
which display distinct physical properties and chemical reactivities. A molecule containing …

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

I Bahar, TR Lezon, A Bakan, IH Shrivastava - Chemical reviews, 2010 - ACS Publications
A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

[图书][B] Computational neuroscience: a comprehensive approach

J Feng - 2003 - taylorfrancis.com
How does the brain work? After a century of research, we still lack a coherent view of how
neurons process signals and control our activities. But as the field of computational …

[HTML][HTML] Computer simulations of membrane proteins

WL Ash, MR Zlomislic, EO Oloo, DP Tieleman - Biochimica et Biophysica …, 2004 - Elsevier
Computer simulations are rapidly becoming a standard tool to study the structure and
dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased …

Molecular dynamics simulations of proteins in lipid bilayers

J Gumbart, Y Wang, A Aksimentiev… - Current opinion in …, 2005 - Elsevier
With recent advances in X-ray crystallography of membrane proteins promising many new
high-resolution structures, molecular dynamics simulations will become increasingly …

Human infrared vision is triggered by two-photon chromophore isomerization

G Palczewska, F Vinberg… - Proceedings of the …, 2014 - National Acad Sciences
Vision relies on photoactivation of visual pigments in rod and cone photoreceptor cells of the
retina. The human eye structure and the absorption spectra of pigments limit our visual …

G-protein coupled receptors: advances in simulation and drug discovery

Y Miao, JA McCammon - Current opinion in structural biology, 2016 - Elsevier
Highlights•GPCRs mediate cellular signaling and represent important drug targets.•A review
on molecular dynamics simulations and drug discovery of GPCRs is presented.•Remarkable …

Theoretical studies on the color-tuning mechanism in retinal proteins

K Fujimoto, S Hayashi, J Hasegawa… - Journal of chemical …, 2007 - ACS Publications
The excited states of the three retinal proteins, bovine rhodopsin (Rh), bacteriorhodopsin
(bR), and sensory rhodopsin II (sRII) were studied using the symmetry-adapted cluster …