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-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 …
CHARMM at 45: Enhancements in accessibility, functionality, and speed
W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
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 …
MMM: A toolbox for integrative structure modeling
G Jeschke - Protein Science, 2018 - Wiley Online Library
Structural characterization of proteins and their complexes may require integration of
restraints from various experimental techniques. MMM (Multiscale Modeling of …
restraints from various experimental techniques. MMM (Multiscale Modeling of …
The contribution of modern EPR to structural biology
G Jeschke - Emerging Topics in Life Sciences, 2018 - portlandpress.com
Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin
labelling is applicable to biomolecules and their complexes irrespective of system size and …
labelling is applicable to biomolecules and their complexes irrespective of system size and …
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference
More than 100,000 protein structures are now known at atomic detail. However, far more are
not yet known, particularly among large or complex proteins. Often, experimental information …
not yet known, particularly among large or complex proteins. Often, experimental information …
Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter
D Del Alamo, L DeSousa, RM Nair… - Proceedings of the …, 2022 - National Acad Sciences
The Amino Acid–Polyamine-Organocation (APC) transporter GadC contributes to the
survival of pathogenic bacteria under extreme acid stress by exchanging extracellular …
survival of pathogenic bacteria under extreme acid stress by exchanging extracellular …
Resolving dynamics and function of transient states in single enzyme molecules
H Sanabria, D Rodnin, K Hemmen, TO Peulen… - Nature …, 2020 - nature.com
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action
by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by …
by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by …
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 …
Cryo-EM structures of the magnesium channel CorA reveal symmetry break upon gating
CorA, the major Mg 2+ uptake system in prokaryotes, is gated by intracellular Mg 2+(KD∼ 1–
2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg 2+ …
2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg 2+ …