ArticleJournal of biomolecular NMR2015
Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 40 citations in OpenAlex.
- NMR data processing, visualization, analysis and structure calculation with NMRFx.Communications chemistry · 2025Article
- Application of NMR to Large RNAs.Journal of molecular biology · 2025Review
- Relaxation Optimized Heteronuclear Experiments for Extending the Size Limit of RNA Nuclear Magnetic Resonance.Journal of the American Chemical Society · 2025Article
- Role of RNA structural plasticity in modulating HIV-1 genome packaging and translation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Machine Learning IsotropicJournal of chemical theory and computation · 2024Article
- Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.Nature communications · 2023Article
- 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
- NMR Studies of Retroviral Genome Packaging.Viruses · 2020Review
- Structural basis for transcriptional start site control of HIV-1 RNA fate.Science (New York, N.Y.) · 2020Article
- Assigning NMR spectra of RNA, peptides and small organic molecules using molecular network visualization software.Journal of biomolecular NMR · 2019Article
- Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.Wiley interdisciplinary reviews. RNA · 2019Review
- Article
- NMR probing of invisible excited states using selectively labeled RNAs.Journal of biomolecular NMR · 2018Article
- Accurate Measurement of Residual Dipolar Couplings in Large RNAs by Variable Flip Angle NMR.Journal of the American Chemical Society · 2018Article
- Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.Journal of biomolecular NMR · 2018Article
- Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.Structure (London, England : 1993) · 2018Article
- Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment.Nucleic acids research · 2017Article
- Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.Biochemistry · 2017Article
- NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.