Improving the performance of the amber RNA force field by tuning the hydrogen-bonding interactions
Molecular dynamics (MD) simulations became a leading tool for investigation of structural
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …
Fine-tuning of the AMBER RNA force field with a new term adjusting interactions of terminal nucleotides
V Mlýnský, P Kührová, T Kühr… - Journal of chemical …, 2020 - ACS Publications
Determination of RNA structural-dynamic properties is challenging for experimental
methods. Thus, atomistic molecular dynamics (MD) simulations represent a helpful …
methods. Thus, atomistic molecular dynamics (MD) simulations represent a helpful …
Simple adjustment of intranucleotide base-phosphate interaction in the ol3 amber force field improves RNA simulations
Molecular dynamics (MD) simulations represent an established tool to study RNA
molecules. The outcome of MD studies depends, however, on the quality of the force field …
molecules. The outcome of MD studies depends, however, on the quality of the force field …
Automatic learning of hydrogen-bond fixes in the AMBER RNA force field
T Frohlking, V Mlýnský, M Janeček… - Journal of Chemical …, 2022 - ACS Publications
The capability of current force fields to reproduce RNA structural dynamics is limited. Several
methods have been developed to take advantage of experimental data in order to enforce …
methods have been developed to take advantage of experimental data in order to enforce …
Benchmarking AMBER force fields for RNA: Comparisons to NMR spectra for single-stranded r (GACC) are improved by revised χ torsions
I Yildirim, HA Stern, JD Tubbs… - The journal of …, 2011 - ACS Publications
Accurately modeling unpaired regions of RNA is important for predicting structure, dynamics,
and thermodynamics of folded RNA. Comparisons between NMR data and molecular …
and thermodynamics of folded RNA. Comparisons between NMR data and molecular …
Combining simulations and solution experiments as a paradigm for RNA force field refinement
Recent computational efforts have shown that the current potential energy models used in
molecular dynamics are not accurate enough to describe the conformational ensemble of …
molecular dynamics are not accurate enough to describe the conformational ensemble of …
Toward convergence in folding simulations of RNA tetraloops: Comparison of enhanced sampling techniques and effects of force field modifications
Atomistic molecular dynamics simulations represent an established technique for
investigation of RNA structural dynamics. Despite continuous development, contemporary …
investigation of RNA structural dynamics. Despite continuous development, contemporary …
UUCG RNA tetraloop as a formidable force-field challenge for MD simulations
Explicit solvent atomistic molecular dynamics (MD) simulations represent an established
technique to study structural dynamics of RNA molecules and an important complement for …
technique to study structural dynamics of RNA molecules and an important complement for …
RNA force field with accuracy comparable to state-of-the-art protein force fields
Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an
atomic level of detail the conformational changes undergone by proteins. The application of …
atomic level of detail the conformational changes undergone by proteins. The application of …
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
Recent modifications and improvements to standard nucleic acid force fields have attempted
to fix problems and issues that have been observed as longer timescale simulations have …
to fix problems and issues that have been observed as longer timescale simulations have …