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Found 12 papers, 5 papers with code
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Importantly, our research identifies hydration of the binding pocket as giving only a minor contribution to the binding free energy and emphasizes the critical importance of precisely tuning force-field parameters to experimental data.
RNA Dynamics from Experimental and Computational Approaches
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis.
Molecular dynamics simulations of chemically modified ribonucleotides
In the context of RNA chemical modifications, alchemical simulations where a wild type nucleotide is converted to a modified one are particularly common.
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules.
Combining simulations and experiments to investigate RNA dynamics
Conformational dynamics is crucial for ribonucleic acid (RNA) function.
Molecular simulations matching denaturation experiments for N6-Methyladenosine
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics.
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure.
Pressure control using stochastic cell rescaling
Molecular dynamics simulations require barostats to be performed at constant pressure.
Computational Physics Statistical Mechanics Chemical Physics
Machine learning a model for RNA structure prediction
Here, we build a set of models that combine thermodynamic parameters, chemical probing data (DMS, SHAPE), and co-evolutionary data (Direct Coupling Analysis, DCA) through a network that outputs perturbations to the ensemble free energy.
The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models
We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence.
Computational Physics Statistical Mechanics Biological Physics Chemical Physics Biomolecules
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations.
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular Dynamics
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids.
Biological Physics Computational Physics Biomolecules
