Empirical Corrections to the Amber RNA Force Field with Target Metadynamics

@article{GilLey2016EmpiricalCT,
  title={Empirical Corrections to the Amber RNA Force Field with Target Metadynamics},
  author={Alejandro Gil-Ley and Sandro Bottaro and G. Bussi},
  journal={Journal of Chemical Theory and Computation},
  year={2016},
  volume={12},
  pages={2790 - 2798}
}
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics… Expand
34 Citations
Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement.
  • 57
  • PDF
Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field.
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics
  • 35
  • PDF
Free Energy Landscape of GAGA and UUCG RNA Tetraloops.
  • 44
  • PDF
RNA force field with accuracy comparable to state-of-the-art protein force fields
  • 75
  • PDF
Development and Testing of the OPLS-AA/M Force Field for RNA.
  • 9
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
  • 147
  • PDF
...
1
2
3
4
...

References

SHOWING 1-10 OF 116 REFERENCES
RNA folding pathways in stop motion
  • 28
  • PDF
...
1
2
3
4
5
...