title: Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.
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.
authors.affiliation: Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Brown
authors.affiliation: Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.|Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Summers
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA. bruce.johnson@asrc.cuny.edu.|One Moon Scientific, Inc., 839 Grant Ave., Westfield, NJ, 07090, USA. bruce.johnson@asrc.cuny.edu.|CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA. bruce.johnson@asrc.cuny.edu.
authors.forename: Bruce A
authors.identifier: http://orcid.org/0000-0001-8445-5368
authors.initials: BA
authors.lastname: Johnson
mesh_terms: D001331:Automation; D002138:Calibration; D002244:Carbon / Q000737:chemistry*; D057225:Data Mining; D019992:Databases as Topic; D006859:Hydrogen / Q000737:chemistry*; D016247:Information Storage and Retrieval; D009711:Nucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D012044:Regression Analysis; D060388:Support Vector Machine
chemical_list: D009711:Nucleotides; D012313:RNA; D002244:Carbon; D006859:Hydrogen
keywords: Chemical shift; NMR signal assignment and validation; RNA; Secondary structure