[HTML][HTML] RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Šponer, G Bussi, M Krepl, P Banáš… - Chemical …, 2018‏ - pmc.ncbi.nlm.nih.gov
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 …

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

DJ Huggins, PC Biggin, MA Dämgen… - Wiley …, 2019‏ - Wiley Online Library
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …

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 …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018‏ - ACS Publications
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 …

Predicting DNA structure using a deep learning method

J Li, TP Chiu, R Rohs - Nature communications, 2024‏ - nature.com
Understanding the mechanisms of protein-DNA binding is critical in comprehending gene
regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key …

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 …

Multiscale simulation of DNA

PD Dans, J Walther, H Gómez, M Orozco - Current opinion in structural …, 2016‏ - Elsevier
Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …

How accurate are accurate force-fields for B-DNA?

PD Dans, I Ivani, A Hospital, G Portella… - Nucleic Acids …, 2017‏ - academic.oup.com
Last generation of force-fields are raising expectations on the quality of molecular dynamics
(MD) simulations of DNA, as well as to the belief that theoretical models can substitute …

The structural impact of DNA mismatches

G Rossetti, PD Dans, I Gomez-Pinto, I Ivani… - Nucleic acids …, 2015‏ - academic.oup.com
The structure and dynamics of all the transversion and transition mismatches in three
different DNA environments have been characterized by molecular dynamics simulations …

Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

B Feng, RP Sosa, AKF Mårtensson, K Jiang… - Proceedings of the …, 2019‏ - pnas.org
Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report
the discovery of specific unstacking effects in certain semihydrophobic environments. Water …