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[HTML][HTML] 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 …
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …
molecules and their interactions. Detailed, physics‐based simulation methods are …
Assessing the current state of amber force field modifications for DNA
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 …
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 …
Predicting DNA structure using a deep learning method
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 …
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
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 …
Multiscale simulation of DNA
Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …
How accurate are accurate force-fields for B-DNA?
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 …
(MD) simulations of DNA, as well as to the belief that theoretical models can substitute …
The structural impact of DNA mismatches
The structure and dynamics of all the transversion and transition mismatches in three
different DNA environments have been characterized by molecular dynamics simulations …
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 …
the discovery of specific unstacking effects in certain semihydrophobic environments. Water …