Molecular dynamics: survey of methods for simulating the activity of proteins
The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
Empirical force fields for biological macromolecules: overview and issues
AD MacKerell Jr - Journal of computational chemistry, 2004 - Wiley Online Library
Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
Vapor-assisted deposition of highly efficient, stable black-phase FAPbI3 perovskite solar cells
INTRODUCTION Metal halide perovskite solar cells (PSCs) have reached a power-
conversion efficiency (PCE) of 25.2%, thus exceeding other thin-film solar cells. FAPbI3 …
conversion efficiency (PCE) of 25.2%, thus exceeding other thin-film solar cells. FAPbI3 …
QuantumATK: an integrated platform of electronic and atomic-scale modelling tools
QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by
professional software engineers in collaboration with academic researchers. While different …
professional software engineers in collaboration with academic researchers. While different …
Beyond shielding: the roles of glycans in the SARS-CoV-2 spike protein
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 …
coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 …
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
Multiple rereads of single proteins at single–amino acid resolution using nanopores
A proteomics tool capable of identifying single proteins would be important for cell biology
research and applications. Here, we demonstrate a nanopore-based single-molecule …
research and applications. Here, we demonstrate a nanopore-based single-molecule …
CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations
CHARMM‐GUI Membrane Builder, http://www. charmm‐gui. org/input/membrane, is a web‐
based user interface designed to interactively build all‐atom protein/membrane or …
based user interface designed to interactively build all‐atom protein/membrane or …
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types
A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed
and applied to phospholipid bilayers with both choline and ethanolamine containing head …
and applied to phospholipid bilayers with both choline and ethanolamine containing head …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …