The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
Open accessAbstract
Significance: We report atomistic simulations describing the spontaneous folding of three RNA tetraloops from the unfolded state to within 1–3 Å of their experimentally determined structures. These common and highly stable motifs serve as building blocks for large structured RNA molecules. This success is caused by the reparameterization of the energy function used to describe the interatomic interactions, which was obtained by calibrating the energy function to reproduce known thermodynamic and kinetic measurements of RNA monomers and dimers. In particular, the accurate recapitulation of the characteristic loop configurations responsible for the thermodynamic hyperstability of these motifs represents a significant milestone to the accurate description of RNA tertiary structure using unbiased all-atom molecular dynamics simulations.
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Cited by
Martini coarse-grained force field: Extension to RNA
Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.05.043 · Cited by 259
Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
Riesenberg, S., Helmbrecht, N., Kanis, P., Maricic, T., & Pääbo, S. (2022) · Nature Communications · doi:10.1038/s41467-022-28137-7 · Cited by 109
Distinguishing Biomolecular Pathways and Metastable States
Oliveira, A. B., Yang, H., Whitford, P. C., & Leite, V. B. P. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00704 · Cited by 38
Computational DNA binding studies of (–)-epigallocatechin-3-gallate
Galindo-Murillo, R., & Cheatham, T. E. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2017.1389306 · Cited by 27
Metadata
- Authors
- Chen, A. A., & García, A. E.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2013-09-16
- Volume
- 110
- Issue
- 42
- Pages
- 16820-16825
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2038354555
- Cited by
- 289
- References
- 36
- FWCI
- 12.24
- Type
- journal article
- Language
- en
- Open access
- bronze
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