The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
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[1] W. Kabsch. A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .
[2] N. Leontis,et al. NMR evidence for dynamic secondary structure in helices II and III of the RNA of Escherichia coli. , 1986, Biochemistry.
[3] H. Varmus,et al. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression , 1988, Nature.
[4] J. Ebel,et al. Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. , 1990, Biochimie.
[5] G Lapalme,et al. The combination of symbolic and numerical computation for three-dimensional modeling of RNA. , 1991, Science.
[6] E. Westhof,et al. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. , 1991, Journal of molecular biology.
[7] R D Klausner,et al. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure. , 1993, Nucleic acids research.
[8] K. Flaherty,et al. Three-dimensional structure of a hammerhead ribozyme , 1994, Nature.
[9] Elizabeth C. Theil,et al. The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study , 1995, Nucleic Acids Res..
[10] M. Hentze,et al. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[11] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[12] J. Williamson. Induced fit in RNA–protein recognition , 2000, Nature Structural Biology.
[13] D. Giedroc,et al. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting1 , 2000, Journal of Molecular Biology.
[14] R. Gutell,et al. The accuracy of ribosomal RNA comparative structure models. , 2002, Current opinion in structural biology.
[15] Eric Westhof,et al. The non-Watson-Crick base pairs and their associated isostericity matrices. , 2002, Nucleic acids research.
[16] Sean R. Eddy,et al. Rfam: an RNA family database , 2003, Nucleic Acids Res..
[17] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[18] K. Weeks,et al. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). , 2005, Journal of the American Chemical Society.
[19] Changbong Hyeon,et al. Extracting stacking interaction parameters for RNA from the data set of native structures. , 2005, Journal of molecular biology.
[20] Eric Westhof,et al. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments , 2005, Nucleic acids research.
[21] D. Fourmy,et al. Structure of the RNA signal essential for translational frameshifting in HIV-1. , 2005, Journal of molecular biology.
[22] D. W. Staple,et al. Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. , 2005, Journal of molecular biology.
[23] Sean R. Eddy,et al. Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..
[24] David L. Wheeler,et al. GenBank , 2015, Nucleic Acids Res..
[25] E. Westhof,et al. Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site , 2006, Nucleic acids research.
[26] D. Case,et al. Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA. , 2006, Journal of molecular biology.
[27] Angela N. Brooks,et al. Structural Basis for Double-Stranded RNA Processing by Dicer , 2006, Science.
[28] François Major,et al. Automated extraction and classification of RNA tertiary structure cyclic motifs , 2006, Nucleic acids research.
[29] D. Turner,et al. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. , 2006, Biochemistry.
[30] David H Mathews,et al. Revolutions in RNA secondary structure prediction. , 2006, Journal of molecular biology.
[31] Byoung-Tak Zhang,et al. Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex , 2006, Cell.
[32] Stijn van Dongen,et al. miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..
[33] Serafim Batzoglou,et al. CONTRAfold: RNA secondary structure prediction without physics-based models , 2006, ISMB.
[34] David H Mathews,et al. Prediction of RNA secondary structure by free energy minimization. , 2006, Current opinion in structural biology.
[35] Wojciech Kasprzak,et al. Bridging the gap in RNA structure prediction. , 2007, Current opinion in structural biology.
[36] P. Stadler,et al. RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription , 2007, Science.
[37] D. Baker,et al. Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.
[38] Elizabeth C. Theil,et al. The family of iron responsive RNA structures regulated by changes in cellular iron and oxygen , 2007, Cellular and Molecular Life Sciences.
[39] A. Krol,et al. An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery , 2007, Nucleic acids research.