ArticleThe journal of physical chemistry. B2014
A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- NMR data processing, visualization, analysis and structure calculation with NMRFx.Communications chemistry · 2025Article
- Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor.Nature communications · 2023Article
- Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.RNA (New York, N.Y.) · 2022Article
- Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields.Life (Basel, Switzerland) · 2022Article
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states.Nature communications · 2021Article
- Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.RNA (New York, N.Y.) · 2020Article
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- Assigning NMR spectra of RNA, peptides and small organic molecules using molecular network visualization software.Journal of biomolecular NMR · 2019Article
- Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.Biophysical journal · 2019Article
- Article
- Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.PLoS computational biology · 2018Article
- Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment.Nucleic acids research · 2017Article
- Article
- Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.Journal of biomolecular NMR · 2015Article
- Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance RProgress in nuclear magnetic resonance spectroscopyReview
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We introduce a simple and fast approach for predicting RNA chemical shifts from interatomic distances that performs with an accuracy similar to existing predictors and enables the first chemical shift-restrained simulations of RNA to be carried out. Our analysis demonstrates that the applied restraints can effectively guide conformational sampling toward regions of space that are more consistent with chemical shifts than the initial coordinates used for the simulations. As such, our approach should be widely applicable in mapping the conformational landscape of RNAs via chemical shift-guided molecular dynamics simulations. The simplicity and demonstrated sensitivity to three-dimensional structure should also allow our method to be used in chemical shift-based RNA structure prediction, validation, and refinement.
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