Principles of protein structural ensemble determination
Highlights•The principles of protein structural ensemble determination are described.•The
use of experimental data averaged over multiple states is analysed.•Approaches for …
use of experimental data averaged over multiple states is analysed.•Approaches for …
CHARMM‐GUI 10 years for biomolecular modeling and simulation
CHARMM‐GUI, http://www. charmm-gui. org, is a web‐based graphical user interface that
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …
CHARMM at 45: Enhancements in accessibility, functionality, and speed
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …
computational biochemistry and biophysics. Commensurate with the developments in …
CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues
Abstract CHARMM-GUI, http://www. charmm-gui. org, is a web-based graphical user
interface to prepare molecular simulation systems and input files to facilitate the usage of …
interface to prepare molecular simulation systems and input files to facilitate the usage of …
The Double‐Histidine Cu2+‐Binding Motif: A Highly Rigid, Site‐Specific Spin Probe for Electron Spin Resonance Distance Measurements
TF Cunningham, MR Putterman, A Desai… - Angewandte …, 2015 - Wiley Online Library
The development of ESR methods that measure long‐range distance distributions has
advanced biophysical research. However, the spin labels commonly employed are highly …
advanced biophysical research. However, the spin labels commonly employed are highly …
Combining experiments and simulations using the maximum entropy principle
W Boomsma, J Ferkinghoff-Borg… - PLoS computational …, 2014 - journals.plos.org
A key component of computational biology is to compare the results of computer modelling
with experimental measurements. Despite substantial progress in the models and …
with experimental measurements. Despite substantial progress in the models and …
Drude polarizable force field for molecular dynamics simulations of saturated and unsaturated zwitterionic lipids
Additive force fields are designed to account for induced electronic polarization in a mean-
field average way, using effective empirical fixed charges. The limitation of this …
field average way, using effective empirical fixed charges. The limitation of this …
Conformational dynamics of ligand-dependent alternating access in LeuT
The leucine transporter (LeuT) from Aquifex aeolicus is a bacterial homolog of
neurotransmitter/sodium symporters (NSSs) that catalyze reuptake of neurotransmitters at …
neurotransmitter/sodium symporters (NSSs) that catalyze reuptake of neurotransmitters at …
Determination of protein structural ensembles using cryo-electron microscopy
M Bonomi, M Vendruscolo - Current Opinion in Structural Biology, 2019 - Elsevier
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated
by the knowledge of their structures, thermodynamics and dynamics. All this information can …
by the knowledge of their structures, thermodynamics and dynamics. All this information can …
Gating topology of the proton-coupled oligopeptide symporters
PW Fowler, M Orwick-Rydmark, S Radestock, N Solcan… - Structure, 2015 - cell.com
Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of
membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport …
membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport …