Folding kinetics of large RNAs.
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Michael T. Wolfinger | Andrea Tanzer | P. Stadler | I. Hofacker | M. Middendorf | C. Flamm | C. Thurner | Michael Geis | C. Mandl
[1] I. Hofacker,et al. Beyond energy minimization: approaches to the kinetic folding of RNA , 2008 .
[2] Rolf Backofen,et al. Variations on RNA folding and alignment: lessons from Benasque , 2007, Journal of mathematical biology.
[3] Tao Pan,et al. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures , 2007, Proceedings of the National Academy of Sciences.
[4] C. Yanofsky,et al. RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria. , 2007, RNA.
[5] Lydia Tapia,et al. Tools for Simulating and Analyzing RNA Folding Kinetics , 2007, RECOMB.
[6] Shi-Jie Chen,et al. Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. , 2007, Journal of molecular biology.
[7] E. Wagner,et al. RNA antitoxins. , 2007, Current opinion in microbiology.
[8] Tao Pan,et al. RNA folding during transcription. , 2006, Annual review of biophysics and biomolecular structure.
[9] Andrey A. Mironov,et al. Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA , 2006, J. Bioinform. Comput. Biol..
[10] Song Cao,et al. Predicting RNA folding thermodynamics with a reduced chain representation model. , 2005, RNA.
[11] Paul Gollnick,et al. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. , 2005, Annual review of genetics.
[12] D. Crothers,et al. The kinetics of ligand binding by an adenine-sensing riboswitch. , 2005, Biochemistry.
[13] Michael T. Wolfinger,et al. Efficient computation of RNA folding dynamics , 2004 .
[14] P. Schuster,et al. Statistics of RNA melting kinetics , 2004, European Biophysics Journal.
[15] M. Gelfand,et al. Riboswitches: the oldest mechanism for the regulation of gene expression? , 2004, Trends in genetics : TIG.
[16] R. Micura,et al. On Secondary Structure Rearrangements and Equilibria of Small RNAs , 2003, Chembiochem : a European journal of chemical biology.
[17] Ali Nahvi,et al. An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.
[18] Peter F. Stadler,et al. Exact Folding Dynamics of RNA Secondary Structures , 2003 .
[19] C. Pleij,et al. Self-induced structural switches in RNA. , 2002, Biochimie.
[20] C. Yanofsky,et al. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.
[21] Michael T. Wolfinger,et al. Barrier Trees of Degenerate Landscapes , 2002 .
[22] Nan Yu,et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.
[23] J. van Duin,et al. Translational control by delayed RNA folding: identification of the kinetic trap. , 2001, RNA.
[24] P. Stadler,et al. Design of multistable RNA molecules. , 2001, RNA.
[25] D. Thirumalai,et al. Early events in RNA folding. , 2001, Annual review of physical chemistry.
[26] P. Higgs. RNA secondary structure: physical and computational aspects , 2000, Quarterly Reviews of Biophysics.
[27] D. Bartel,et al. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. , 2000, Science.
[28] E. Siggia,et al. Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[29] P. Stadler,et al. Design of Multi-Stable RNA Molecules , 2000 .
[30] P. Schuster,et al. RNA folding at elementary step resolution. , 1999, RNA.
[31] C. Pleij,et al. Metastable structures and refolding kinetics in hok mRNA of plasmid R1. , 1999, RNA.
[32] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[33] M Cieplak,et al. Energy landscapes, supergraphs, and "folding funnels" in spin systems. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[34] J. Doye,et al. Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters , 1999, cond-mat/9903305.
[35] P. Schuster,et al. Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.
[36] Mark A. Miller,et al. Archetypal energy landscapes , 1998, Nature.
[37] A. T. Perrotta,et al. A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation. , 1998, Journal of molecular biology.
[38] P. Higgs,et al. Barrier heights between ground states in a model of RNA secondary structure , 1998 .
[39] A. Gultyaev,et al. Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3'-end triggers structural rearrangements that allow translation and antisense RNA binding. , 1997, Journal of molecular biology.
[40] R. Poot,et al. RNA folding kinetics regulates translation of phage MS2 maturation gene. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[41] Detlev Riesner,et al. Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation , 1997, The EMBO journal.
[42] M. Karplus,et al. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics , 1997 .
[43] E. Westhof,et al. Hierarchy and dynamics of RNA folding. , 1997, Annual review of biophysics and biomolecular structure.
[44] Paul Higgs,et al. Evidence for kinetic effects in the folding of large RNA molecules , 1996 .
[45] J. van Duin,et al. RNA phage KU1 has an insertion of 18 nucleotides in the start codon of its lysis gene. , 1996, Virology.
[46] G. Steger,et al. Description of RNA folding by "simulated annealing". , 1996, Journal of molecular biology.
[47] K. Dill,et al. Statistical thermodynamics of double‐stranded polymer molecules , 1995 .
[48] P. Frantsuzov,et al. Statistical description of nucleic acid secondary structure folding. , 1995, Journal of biomolecular structure & dynamics.
[49] C. Pleij,et al. The computer simulation of RNA folding pathways using a genetic algorithm. , 1995, Journal of molecular biology.
[50] J. van Duin,et al. Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? , 1995, RNA.
[51] P. Higgs. Thermodynamic properties of transfer RNA: a computational study , 1995 .
[52] T. H. Klotz,et al. "Valley structures" in the phase space of a finite 3d ISING spin glass with , 1994 .
[53] Walter Fontana,et al. Fast folding and comparison of RNA secondary structures , 1994 .
[54] J. van Duin,et al. Translational control by a long range RNA-RNA interaction; a basepair substitution analysis. , 1993, Nucleic acids research.
[55] T. H. Klotz,et al. "valley Structures" in the Phase Space of a Nite 3d Ising Spin Glass with I Inter- Actions , 1993 .
[56] R. Luce,et al. In vitro recombination and terminal elongation of RNA by Q beta replicase. , 1992, The EMBO journal.
[57] A. Gultyaev,et al. The computer simulation of RNA folding involving pseudoknot formation. , 1991, Nucleic acids research.
[58] J. Abrahams,et al. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. , 1990, Nucleic acids research.
[59] J. van Duin,et al. Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance. , 1990, Journal of molecular biology.
[60] M. Zuker. On finding all suboptimal foldings of an RNA molecule. , 1989, Science.
[61] L. Frost,et al. The physiology and biochemistry of pili. , 1988, Advances in microbial physiology.
[62] B. Berkhout,et al. Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene. , 1987, Journal of molecular biology.
[63] S. Molin,et al. Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[64] A A Mironov,et al. A kinetic approach to the prediction of RNA secondary structures. , 1985, Journal of biomolecular structure & dynamics.
[65] H. M. Martinez,et al. An RNA folding rule , 1984, Nucleic Acids Res..
[66] D. Sankoff,et al. RNA secondary structures and their prediction , 1984 .
[67] R. Contreras,et al. A-Protein gene of bacteriophage MS2 , 1975, Nature.
[68] W. Olson,et al. Configurational statistics of polynucleotide chains. A single virtual bond treatment. , 1975, Macromolecules.
[69] D. Crothers,et al. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. , 1974, Journal of molecular biology.
[70] W. Fiers,et al. Nucleotide Sequence of the Gene Coding for the Bacteriophage MS2 Coat Protein , 1972, Nature.
[71] M. Eigen,et al. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. , 1971, Journal of molecular biology.
[72] M. Eigen,et al. Co-operative non-enzymic base recognition. I. Thermodynamics of the helix-coil transition of oligoriboadenylic acids at ACIDIC PH. , 1970, Journal of molecular biology.