Database proton NMR chemical shifts for RNA signal assignment and validation

[1]  Dipali G. Sashital,et al.  Structure of the yeast U2/U6 snRNA complex. , 2012, RNA.

[2]  M. Summers,et al.  Identification of a minimal region of the HIV-1 5'-leader required for RNA dimerization, NC binding, and packaging. , 2012, Journal of molecular biology.

[3]  Arash Bahrami,et al.  RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts , 2012, Journal of biomolecular NMR.

[4]  F. Allain,et al.  A procedure to validate and correct the 13C chemical shift calibration of RNA datasets , 2012, Journal of Biomolecular NMR.

[5]  F. Allain,et al.  Isotope labeling and segmental labeling of larger RNAs for NMR structural studies. , 2012, Advances in experimental medicine and biology.

[6]  N. Shankar,et al.  An equilibrium-dependent retroviral mRNA switch regulates translational recoding , 2011, Nature.

[7]  Xiao Heng,et al.  NMR Detection of Structures in the HIV-1 5′-Leader RNA That Regulate Genome Packaging , 2011, Science.

[8]  M. Summers,et al.  Structural determinants and mechanism of HIV-1 genome packaging. , 2011, Journal of molecular biology.

[9]  Rhiju Das,et al.  Understanding the errors of SHAPE-directed RNA structure modeling. , 2011, Biochemistry.

[10]  W. Chiu,et al.  Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. , 2010, Journal of molecular biology.

[11]  Jinbu Wang,et al.  Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. , 2010, Methods.

[12]  D. Case,et al.  Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H–13C residual dipolar coupling on refinement , 2010, Journal of biomolecular NMR.

[13]  K. Weeks.  Advances in RNA structure analysis by chemical probing. , 2010, Current opinion in structural biology.

[14]  S. L. Lam,et al.  Use of chemical shifts for structural studies of nucleic acids. , 2010, Progress in nuclear magnetic resonance spectroscopy.

[15]  M. Summers,et al.  Isotope labeling strategies for NMR studies of RNA , 2009, Journal of biomolecular NMR.

[16]  Charles D Schwieters,et al.  A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. , 2009, Journal of molecular biology.

[17]  C. Ponting,et al.  Evolution and Functions of Long Noncoding RNAs , 2009, Cell.

[18]  D. Herschlag,et al.  Metal ion-based RNA cleavage as a structural probe. , 2009, Methods in enzymology.

[19]  O. Ohlenschläger,et al.  Conformational signatures of 13C chemical shifts in RNA ribose , 2008, Journal of biomolecular NMR.

[20]  Ad Bax,et al.  Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data , 2008, Journal of biomolecular NMR.

[21]  S. Wijmenga,et al.  Multiple segmental and selective isotope labeling of large RNA for NMR structural studies , 2008, Nucleic acids research.

[22]  David S. Wishart,et al.  CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data , 2008, Nucleic Acids Res..

[23]  H. Urlaub,et al.  Isolation of an active step I spliceosome and composition of its RNP core , 2008, Nature.

[24]  Oliver F. Lange,et al.  Consistent blind protein structure generation from NMR chemical shift data , 2008, Proceedings of the National Academy of Sciences.

[25]  T. Steitz.  A structural understanding of the dynamic ribosome machine , 2008, Nature Reviews Molecular Cell Biology.

[26]  C. Schwieters,et al.  Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. , 2008, Journal of the American Chemical Society.

[27]  Teresa Carlomagno,et al.  13C-detection in RNA bases: revealing structure-chemical shift relationships. , 2007, Journal of the American Chemical Society.

[28]  Catherine A. Wakeman,et al.  Structural features of metabolite-sensing riboswitches. , 2007, Trends in biochemical sciences.

[29]  H. Noller,et al.  The ribosome in focus: new structures bring new insights. , 2007, Trends in biochemical sciences.

[30]  F. Boisvert,et al.  The multifunctional nucleolus , 2007, Nature Reviews Molecular Cell Biology.

[31]  Michele Vendruscolo,et al.  Protein structure determination from NMR chemical shifts , 2007, Proceedings of the National Academy of Sciences.

[32]  A. Ferré-D’Amaré,et al.  Riboswitches: small-molecule recognition by gene regulatory RNAs. , 2007, Current opinion in structural biology.

[33]  M. Summers,et al.  Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein: μΨ RNA Packaging Signal Complex , 2007 .

[34]  Olivier Voinnet,et al.  The diversity of RNA silencing pathways in plants. , 2006, Trends in genetics : TIG.

[35]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[36]  M. Hennig,et al.  A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[37]  L. Scott,et al.  RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. , 2005, Journal of molecular biology.

[38]  K. Schulze-Osthoff,et al.  Regulation of apoptosis by alternative pre-mRNA splicing. , 2005, Molecular cell.

[39]  Kim Vn,et al.  Small RNAs: classification, biogenesis, and function. , 2005, Molecules and cells.

[40]  J. Puglisi,et al.  Structure determination of large biological RNAs. , 2005, Methods in enzymology.

[41]  V. Kim,et al.  Small RNAs : Classification , Biogenesis , and Function , 2005 .

[42]  M. Summers,et al.  Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus , 2004, Nature.

[43]  M. Summers,et al.  NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. , 2004, Journal of molecular biology.

[44]  Yun-Xing Wang,et al.  Periodicity in residual dipolar couplings and nucleic acid structures. , 2004, Journal of the American Chemical Society.

[45]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[46]  C. A. Theimer,et al.  New applications of 2D filtered/edited NOESY for assignment and structure elucidation of RNA and RNA-protein complexes , 2004, Journal of biomolecular NMR.

[47]  Bruce A Johnson,et al.  Using NMRView to visualize and analyze the NMR spectra of macromolecules. , 2004, Methods in molecular biology.

[48]  Joseph D Puglisi,et al.  Structure of HCV IRES domain II determined by NMR , 2003, Nature Structural Biology.

[49]  J. Puglisi,et al.  NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling. , 2002, Journal of the American Chemical Society.

[50]  Yong Wang,et al.  Modeling for Optimal Probability Prediction , 2002, ICML.

[51]  V. L. Rath,et al.  Structure and Function of the Eukaryotic Ribosome The Next Frontier , 2002, Cell.

[52]  S. Wijmenga,et al.  Prediction of proton chemical shifts in RNA – Their use in structure refinement and validation , 2001, Journal of biomolecular NMR.

[53]  P. Rossi,et al.  Dependence of 13C NMR chemical shifts on conformations of rna nucleosides and nucleotides. , 2001, Journal of magnetic resonance.

[54]  M. Vallazza,et al.  Structure of Free Thermus flavus 5 S rRNA at 1.3 nm Resolution from Synchrotron X-ray Solution Scattering* , 2000, The Journal of Biological Chemistry.

[55]  G. Varani,et al.  The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. , 2000, EMBO reports.

[56]  Ian H. Witten,et al.  Data mining: practical machine learning tools and techniques, 3rd Edition , 1999 .

[57]  D. Case,et al.  An empirical analysis of proton chemical shifts in nucleic acids , 1999 .

[58]  G. Varani,et al.  How accurately and precisely can RNA structure be determined by NMR? , 1997, Journal of molecular biology.

[59]  D. Crothers,et al.  Determining RNA solution structure by segmental isotopic labeling and NMR: application to Caenorhabditis elegans spliced leader RNA 1. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[60]  D. Case.  Calibration of ring-current effects in proteins and nucleic acids , 1995, Journal of biomolecular NMR.

[61]  R. Batey,et al.  Preparation of isotopically enriched RNAs for heteronuclear NMR. , 1995, Methods in enzymology.

[62]  S. Yokoyama,et al.  Selective deuteration of RNA for NMR signal assignment. , 1995, Nucleic acids symposium series.

[63]  Bruce A. Johnson,et al.  NMR View: A computer program for the visualization and analysis of NMR data , 1994, Journal of biomolecular NMR.

[64]  D. Wishart,et al.  The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data , 1994, Journal of biomolecular NMR.

[65]  John K. Ousterhout,et al.  Tcl and the Tk Toolkit , 1994 .

[66]  Ad Bax,et al.  Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins , 1993, Journal of biomolecular NMR.

[67]  J. Harper,et al.  Selective isotopic enrichment of synthetic RNA: application to the HIV-1 TAR element. , 1993, Biochemistry.

[68]  J. Puglisi,et al.  Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. , 1992, Nucleic acids research.

[69]  A. Pardi,et al.  Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies. , 1992, Nucleic acids research.

[70]  F. Richards,et al.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. , 1992, Biochemistry.

[71]  A. Pardi,et al.  Three-dimensional heteronuclear NMR studies of RNA , 1992, Nature.

[72]  F. Richards,et al.  Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. , 1991, Journal of molecular biology.

[73]  H. Noller,et al.  Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. , 1988, Methods in enzymology.

[74]  J. Ebel,et al.  Probing the structure of RNAs in solution. , 1987, Nucleic acids research.

[75]  K. Wüthrich.  NMR of proteins and nucleic acids , 1988 .

[76]  J. Bachellerie,et al.  The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. , 1984, Nucleic acids research.

[77]  W. Gilbert,et al.  Chemical probes for higher-order structure in RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.