RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
New developments in force fields for biomolecular simulations
PS Nerenberg, T Head-Gordon - Current opinion in structural biology, 2018 - Elsevier
Highlights•Biomolecular force fields (FFs) have progressed rapidly in the past five
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
[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 …
Assessing the current state of amber force field modifications for DNA
R Galindo-Murillo, JC Robertson… - Journal of chemical …, 2016 - ACS Publications
The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …
dynamics, and interactions has witnessed enormous advances in recent years due to the …
Programming nanoparticle valence bonds with single-stranded DNA encoders
Nature has evolved strategies to encode information within a single biopolymer to program
biomolecular interactions with characteristic stoichiometry, orthogonality and …
biomolecular interactions with characteristic stoichiometry, orthogonality and …
AMOEBA polarizable atomic multipole force field for nucleic acids
The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …
and electrostatic parameters were determined from high-level quantum mechanical data …
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
J Yoo, A Aksimentiev - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly
ordered three-dimensional structures that define their functions. The key to folding of a …
ordered three-dimensional structures that define their functions. The key to folding of a …
Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations
R Galindo-Murillo, TE Cheatham III - Nucleic acids research, 2021 - academic.oup.com
Visualization of double stranded DNA in gels with the binding of the fluorescent dye
ethidium bromide has been a basic experimental technique in any molecular biology …
ethidium bromide has been a basic experimental technique in any molecular biology …
[HTML][HTML] Review of force fields and intermolecular potentials used in atomistic computational materials research
Molecular simulation is a powerful computational tool for a broad range of applications
including the examination of materials properties and accelerating drug discovery. At the …
including the examination of materials properties and accelerating drug discovery. At the …
Development of force field parameters for the simulation of single-and double-stranded DNA molecules and DNA–protein complexes
Although molecular dynamics (MD) simulations have been used extensively to study the
structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based …
structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based …