Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
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[1] Homer Jacobson,et al. Intramolecular Reaction in Polycondensations. I. The Theory of Linear Systems , 1950 .
[2] D. Crothers,et al. Improved estimation of secondary structure in ribonucleic acids. , 1973, Nature: New biology.
[3] C. Woese,et al. 5S RNA secondary structure , 1975, Nature.
[4] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[5] M. Speek,et al. Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25. , 1982, Nucleic acids research.
[6] K Miura,et al. Chemical modification of guanine residues of mouse 5 S ribosomal RNA with kethoxal. (Nucleosides and nucleotides 46). , 1983, Biochimica et biophysica acta.
[7] David Sankoff,et al. RNA secondary structures and their prediction , 1984 .
[8] T. Cech,et al. Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[9] H. Noller,et al. Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. , 1986, Journal of molecular biology.
[10] R. Garrett,et al. Structure and accessibility of domain I of Escherichia coli 23 S RNA in free RNA, in the L24-RNA complex and in 50 S subunits. Implications for ribosomal assembly. , 1987, Journal of molecular biology.
[11] D M Crothers,et al. Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence. , 1987, Biochemistry.
[12] J. Ebel,et al. Probing the structure of RNAs in solution. , 1987, Nucleic acids research.
[13] O. Uhlenbeck,et al. Characterization of RNA hairpin loop stability. , 1988, Nucleic acids research.
[14] G. Knapp. Enzymatic approaches to probing of RNA secondary and tertiary structure. , 1989, Methods in enzymology.
[15] M. Zuker. On finding all suboptimal foldings of an RNA molecule. , 1989, Science.
[16] K. Umesono,et al. Comparative and functional anatomy of group II catalytic introns--a review. , 1989, Gene.
[17] The solution structure of the Escherichia coli initiator tRNA and its interactions with initiation factor 2 and the ribosomal 30 S subunit. , 1989, The Journal of biological chemistry.
[18] E. Westhof,et al. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. , 1990, Journal of molecular biology.
[19] L. Grivell,et al. Structural analysis of a group II intron by chemical modifications and minimal energy calculations. , 1990, Journal of Biomolecular Structure and Dynamics.
[20] S. Gerbi,et al. Changes in 7SL RNA conformation during the signal recognition particle cycle. , 1991, The EMBO journal.
[21] 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.
[22] D. Turner,et al. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops , 1991 .
[23] D. Turner,et al. Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. , 1991, Biochemistry.
[24] D. Turner,et al. Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs. , 1991, Biochemistry.
[25] Daniel P. Romero,et al. A conserved secondary structure for telomerase RNA , 1991, Cell.
[26] I. Tinoco,et al. A thermodynamic study of unusually stable RNA and DNA hairpins. , 1991, Nucleic acids research.
[27] I. Tinoco,et al. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. , 1992, Nucleic acids research.
[28] D. Turner,et al. RNA hairpin loop stability depends on closing base pair. , 1993, Nucleic acids research.
[29] H. Noller,et al. Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits. , 1993, Journal of molecular biology.
[30] D. Turner,et al. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. , 1993, Biochemistry.
[31] A. Tranguch,et al. Structure-sensitive RNA footprinting of yeast nuclear ribonuclease P. , 1994, Biochemistry.
[32] D. Turner,et al. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. , 1994, Biochemistry.
[33] A. E. Walter,et al. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[34] A. E. Walter,et al. The stability and structure of tandem GA mismatches in RNA depend on closing base pairs. , 1994, Biochemistry.
[35] S. Butcher,et al. Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex. , 1994, Journal of molecular biology.
[36] T. Cech,et al. Analysis of the structure of Tetrahymena nuclear RNAs in vivo: telomerase RNA, the self-splicing rRNA intron, and U2 snRNA. , 1995, RNA.
[37] E Westhof,et al. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. , 1995, Journal of molecular biology.
[38] D. Turner,et al. A periodic table of symmetric tandem mismatches in RNA. , 1995, Biochemistry.
[39] D. Turner,et al. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme. , 1995, Biochemistry.
[40] C. Pleij,et al. The computer simulation of RNA folding pathways using a genetic algorithm. , 1995, Journal of molecular biology.
[41] O. Uhlenbeck,et al. Keeping RNA happy. , 1995, RNA.
[42] D. Crothers,et al. In vivo structural analysis of spliced leader RNAs in Trypanosoma brucei and Leptomonas collosoma: a flexible structure that is independent of cap4 methylations. , 1995, RNA.
[43] D H Turner,et al. G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides. , 1996, Biochemistry.
[44] K. Hall,et al. A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. , 1996, Biochemistry.
[45] J. A. Mcdowell,et al. Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA. , 1997, Biochemistry.
[46] O. Nygård,et al. Structure of 18 S Ribosomal RNA in Native 40 S Ribosomal Subunits* , 1997, The Journal of Biological Chemistry.
[47] M. Serra,et al. Improved parameters for the prediction of RNA hairpin stability. , 1997, Biochemistry.
[48] T. Tsuchiya. Eugenic sterilizations in Japan and recent demands for an apology: a report. , 1997, Ethics and intellectual disability.
[49] F. Larimer,et al. Comparative analyses of the secondary structures of synthetic and intracellular yeast MFA2 mRNAs. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[50] F. Michel,et al. Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain V. , 1998, RNA.
[51] P. Borer,et al. Three-dimensional folding of an RNA hairpin required for packaging HIV-1. , 1998, Journal of molecular biology.
[52] T. Pan,et al. Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. , 1998, Nucleic acids research.
[53] M. Serra,et al. Stability of RNA hairpins closed by wobble base pairs. , 1998, Biochemistry.
[54] D. Turner,et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.
[55] E Rivas,et al. A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.
[56] James W. Brown,et al. The Ribonuclease P Database , 1994, Nucleic Acids Res..
[57] D. Turner,et al. Thermodynamics of single mismatches in RNA duplexes. , 1999, Biochemistry.
[58] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[59] P. Schuster,et al. Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.
[60] D. Turner,et al. The energetics of small internal loops in RNA , 1999, Biopolymers.
[61] P. Bevilacqua,et al. Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. , 1999, Biochemistry.
[62] Miroslawa Z. Barciszewska,et al. 5S ribosomal RNA database Y2K , 2000, Nucleic Acids Res..
[63] K. Dill,et al. RNA folding energy landscapes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[64] T. Steitz,et al. The structural basis of ribosome activity in peptide bond synthesis. , 2000, Science.
[65] M. Ares,et al. Use of dimethyl sulfate to probe RNA structure in vivo. , 2000, Methods in enzymology.
[66] D. Turner,et al. Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. , 2000, Biochemistry.
[67] M J Serra,et al. A test of the model to predict unusually stable RNA hairpin loop stability. , 2000, RNA.
[68] J. M. Diamond,et al. Thermodynamics of three-way multibranch loops in RNA. , 2001, Biochemistry.
[69] J. Miranda-Ríos,et al. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[70] A. Lambowitz,et al. Mechanism of maturase‐promoted group II intron splicing , 2001, The EMBO journal.
[71] D H Turner,et al. Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair. , 2001, Biochemistry.
[72] L. Lim,et al. An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.
[73] D H Turner,et al. Thermodynamic stabilities of internal loops with GU closing pairs in RNA. , 2001, Biochemistry.
[74] T. Tuschl,et al. Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.
[75] Michael T. McManus,et al. Gene silencing in mammals by small interfering RNAs , 2002, Nature Reviews Genetics.
[76] Thomas A Steitz,et al. Structural insights into peptide bond formation , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[77] Douglas H. Turner,et al. Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[78] Philip C Bevilacqua,et al. Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. , 2002, Biochemistry.
[79] D. Turner,et al. Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. , 2002, Biochemistry.
[80] Bryan R. Cullen,et al. RNA interference: antiviral defense and genetic tool , 2002, Nature Immunology.
[81] Brent M. Znosko,et al. Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. , 2002, Biochemistry.
[82] K. Weeks,et al. Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA. , 2003, Biochemistry.
[83] C. Lawrence,et al. A statistical sampling algorithm for RNA secondary structure prediction. , 2003, Nucleic acids research.
[84] D. Turner,et al. Uptake and antifungal activity of oligonucleotides in Candida albicans , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[85] Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. , 2003, Biochemistry.
[86] Christian Zwieb,et al. SRPDB: Signal Recognition Particle Database , 2003, Nucleic Acids Res..