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Tag pseudoknots [57 articles]

Recent papers classified by the tag pseudoknots.
  • SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e149.
    by Irmtraud M Meyer, István Miklós
    posted to pseudoknots rna secondary_structure by raylim on 2007-09-20 19:53:04 as *** along with 3 people zwang cabbagezs bertelsen
  • Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
    PNAS, Vol. 97, No. 12. (6 June 2000), pp. 6515-6520.
    by Herve Isambert, Eric D Siggia
    posted to monte-carlo pseudoknots rna rna-folding by Kiarostami on 2007-05-08 01:07:51 as ** along with 3 people austin eckart_bindewald Hosna
  • notes Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.
    Proc Natl Acad Sci U S A, Vol. 100, No. 26. (23 December 2003), pp. 15310-15315.
    by A Xayaphoummine, T Bucher, F Thalmann, H Isambert
    posted to pseudoknots rna rna-secondary-structure by Kiarostami on 2007-05-08 23:43:09 as ** along with 6 people and 3 groups evaf austin marcius arcticrasta condon Hosna beta BioinfoCIPF SGU-CIPF
  • Thermodynamics of Folding of the RNA Pseudoknot of the T4 Gene 32 Autoregulatory Messenger RNA
    Biochemistry, Vol. 35, No. 13. (2 April 1996), pp. 4176-4186.
    by H Qiu, K Kaluarachchi, Z Du, DW Hoffman, DP Giedroc
    posted to pseudoknots data by Hosna on 2007-01-21 23:23:04 as ***
  • Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA
    PNAS, Vol. 100, No. 2. (21 January 2003), pp. 449-454.
    by Carla A Theimer, David L Finger, Lukas Trantirek, Juli Feigon
    posted to pseudoknots data by Hosna on 2007-01-21 23:49:49 as ***
  • RNA Pseudoknots that Inhibit Human Immunodeficiency Virus Type 1 Reverse Transcriptase
    PNAS, Vol. 89, No. 15. (1 August 1992), pp. 6988-6992.
    by C Tuerk, S Macdougal, L Gold
    posted to data pseudoknots by Hosna on 2006-12-19 19:30:59 as **
  • Secondary Structure of Vertebrate Telomerase RNA
    Cell, Vol. 100, No. 5. (3 March 2000), pp. 503-514.
    by Jiunn-Liang Chen, Maria A Blasco, Carol W Greider
    posted to pseudoknots data by Hosna on 2007-01-22 20:42:02 as **** along with 1 person aredash
  • Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function.
    Mol Cell, Vol. 17, No. 5. (4 March 2005), pp. 671-682.
    by CA Theimer, CA Blois, J Feigon
    posted to pseudoknots data by Hosna on 2007-01-21 23:55:39 as *** along with 2 people bpagano physics
  • PseudoBase: structural information on RNA pseudoknots.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 194-195.
    by FH van Batenburg, AP Gultyaev, CW Pleij
    posted to data pseudoknots wabi by Hosna on 2007-01-22 19:48:26 as *** along with 1 person and 1 group condon beta
  • The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
    RNA (New York, N.Y.) (27 March 2008)
    by Zasha Weinberg, Elizabeth E E Regulski, Ming C C Hammond, Jeffrey E E Barrick, Zizhen Yao, Walter L L Ruzzo, Ronald R R Breaker
    posted to pseudoknots by Hosna on 2008-04-22 22:19:40 as ***
  • The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase
    J. Virol., Vol. 71, No. 8. (1 August 1997), pp. 5990-5996.
    by Ba Deiman, Rm Kortlever, Cw Pleij
    posted to pseudoknots data by Hosna on 2007-01-22 20:38:30 as ****
  • Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot
    pp. 545-564.
    by CA Theimer
    posted to pseudoknots data by Hosna on 2007-01-21 23:28:28 as ***
  • Five pseudoknots are present at the 204 nucleotides long 3' noncoding region of tobacco mosak virus RNA
    Nucl. Acids Res., Vol. 13, No. 21. (11 November 1985), pp. 7673-7686.
    by Alex Belkum, Jan P Abrahams, Cornelis W Pleij, Leendert Bosch
    posted to pseudoknots data by Hosna on 2007-01-22 20:50:45 as ****
  • RNA pseudoknots. Stability and loop size requirements.
    J Mol Biol, Vol. 214, No. 2. (20 July 1990), pp. 455-470.
    by JR Wyatt, JD Puglisi, I Tinoco
    posted to pseudoknots data by Hosna on 2007-01-21 23:12:12 as ***
  • Folding of an mRNA Pseudoknot Required for Stop Codon Readthrough: Effects of Mono- and Divalent Ions on Stability
    Biochemistry, Vol. 36, No. 51. (23 December 1997), pp. 16173-16186.
    by TC Gluick, NM Wills, RF Gesteland, DE Draper
    posted to pseudoknots data by Hosna on 2007-01-21 23:35:40 as **
  • The Ribonuclease P Database
    Nucl. Acids Res., Vol. 27, No. 1. (1 January 1999), 314.
    by Jw Brown
    posted to pseudoknots data by Hosna on 2007-01-22 19:32:58 as *** along with 2 people and 1 group arcticrasta condon beta
  • Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting.
    J Mol Biol, Vol. 298, No. 2. (28 April 2000), pp. 167-185.
    by DP Giedroc, CA Theimer, PL Nixon
    posted to pseudoknots data by Hosna on 2007-01-22 20:34:05 as **** along with 2 people and 1 group condon physics beta
  • Equilibrium Unfolding Pathway of an H-type RNA Pseudoknot which Promotes Programmed 1 Ribosomal Frameshifting
    pp. 1283-1299.
    by CA Theimer
    posted to pseudoknots data by Hosna on 2007-01-22 00:02:06 as ***
  • A pseudoknotted RNA oligonucleotide
    Nature, Vol. 331, No. 6153. (21 January 1988), pp. 283-286.
    by Joseph D Puglisi, Jacqueline R Wyatt, Ignacio Tinoco
    posted to pseudoknots data by Hosna on 2007-01-21 23:00:42 as ***
  • Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res, Vol. 26, No. 1. (1 January 1998), pp. 148-153.
    by M Sprinzl, C Horn, M Brown, A Ioudovitch, S Steinberg
    posted to data pseudoknots wabi by Hosna on 2007-01-22 19:27:06 as *** along with 2 people and 1 group evaf condon beta
  • PseudoBase: a database with RNA pseudoknots
    Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 201-204.
    by FHD van Batenburg, AP Gultyaev, CWA Pleij, J Ng, J Oliehoek
    posted to pseudoknots data by Hosna on 2007-01-20 02:14:50 as **** along with 3 people and 3 groups marcius arcticrasta condon beta BioinfoCIPF SGU-CIPF
  • Crystal structure of a hepatitis delta virus ribozyme.
    Nature, Vol. 395, No. 6702. (8 October 1998), pp. 567-574.
    by AR Ferré-D'Amaré, K Zhou, JA Doudna
    posted to pseudoknots data by Hosna on 2007-01-22 20:44:21 as **** along with 1 person and 1 group condon beta
  • Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
    Discrete Appl. Math., Vol. 104, No. 1-3. (2000), pp. 45-62.
    by Tatsuya Akutsu
    posted to folding pseudoknots rna by guxiyou on 2008-03-26 19:33:16 as **
  • Tree adjoining grammars for RNA structure prediction
    Theoretical Computer Science, Vol. 210, No. 2. (17 January 1999), pp. 277-303.
    by Yasuo Uemura, Aki Hasegawa, Satoshi Kobayashi, Takashi Yokomori
    posted to folding pseudoknots rna by guxiyou on 2008-03-26 19:35:41 as ** along with 3 people and 1 group condon Hosna Kiarostami beta
  • Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm
    Comput. Appl. Biosci., Vol. 13, No. 4. (1 August 1997), pp. 459-471.
    by Bruce A Shapiro, Jin C Wu
    posted to base-triple folding genetic pseudoknots rna by guxiyou on 2008-03-26 20:58:47 as **
  • RNA pseudoknot prediction in energy-based models.
    J Comput Biol, Vol. 7, No. 3-4. (2000), pp. 409-427.
    by RB Lyngsø, CN Pedersen
    posted to folding np-hard pseudoknots rna by guxiyou on 2008-03-26 19:38:45 as ** along with 4 people and 1 group evaf arcticrasta condon Hosna beta
  • Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs
    (2001)
    by Samuel Ieong, Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung, Siu-Ming Yiu
    posted to folding pseudoknots rna subset by guxiyou on 2008-03-26 19:40:28 as **
  • Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
    BMC Bioinformatics, Vol. 5 (4 August 2004)
    by J Reeder, R Giegerich
    posted to algebraic-dynamic-programming pseudoknots rna structure by condon to the group beta on 2006-05-18 01:47:52 as ** along with 4 people and 2 groups marcius eckart_bindewald arcticrasta Hosna BioinfoCIPF SGU-CIPF
  • A dynamic programming algorithm for RNA structure prediction including pseudoknots.
    J Mol Biol, Vol. 285, No. 5. (5 February 1999), pp. 2053-2068.
    by E Rivas, SR Eddy
    posted to prediction pseudoknots rna by condon to the group beta on 2006-07-01 05:10:44 as ** along with 9 people evaf balajis eckart_bindewald arcticrasta dquest Hosna jarasch physics guxiyou
  • Profiling and Searching for RNA Pseudoknot Structures in Genomes
    Lecture Notes in Computer Science, Vol. 3515 (January 2005), pp. 968-975.
    by Chunmei Liu, Yinglei Song, Russell L Malmberg, Liming Cai
    posted to discovery pseudoknots rna by condon to the group beta on 2006-06-29 20:35:53 as **
  • Pseudoknots: a new motif in the RNA game.
    Trends Biochem Sci, Vol. 15, No. 4. (April 1990), pp. 143-147.
    by CW Pleij
    posted to pseudoknots review rna by condon to the group beta on 2006-07-02 03:51:54 as **
  • Asymmetry in RNA pseudoknots: observation and theory
    Nucleic Acids Research, Vol. 33, No. 7. (2005), pp. 2210-2214.
    by Daniel P Aalberts, Nathan O Hodas
    posted to energy-model pseudoknots rna by condon to the group beta on 2006-04-14 23:59:21 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • PseudoViewer: automatic visualization of RNA pseudoknots.
    Bioinformatics, Vol. 18 Suppl 1 (2002)
    by K Han, Y Lee, W Kim
    posted to pseudoknots rna visualization by condon to the group beta on 2006-07-01 03:38:27 as ** along with 1 person Hosna
  • Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots,
    Discrete Applied Mathematics, Vol. 104, No. 1-3. (15 August 2000), pp. 45-62.
    by Tatsuya Akutsu
    posted to pseudoknots rna structure by condon to the group beta on 2006-05-18 18:48:12 as ** along with 1 person Hosna
  • The computer simulation of RNA folding pathways using a genetic algorithm.
    J Mol Biol, Vol. 250, No. 1. (30 June 1995), pp. 37-51.
    by AP Gultyaev, FH van Batenburg, CW Pleij
    posted to pseudoknots rna structure by condon to the group beta on 2006-05-31 20:58:36 as ** along with 3 people Climb08 Hosna guxiyou
  • Pseudoknots: RNA structures with diverse functions.
    PLoS Biol, Vol. 3, No. 6. (June 2005)
    by DW Staple, SE Butcher
    posted to pseudoknots review rna structure by condon to the group beta on 2006-05-15 22:19:00 as ** along with 4 people and 2 groups austin marcius arcticrasta Hosna BioinfoCIPF SGU-CIPF
  • Candidates for Novel RNA Topologies
    Journal of Molecular Biology, Vol. 341, No. 5. (27 August 2004), pp. 1129-1144.
    by Namhee Kim, Nahum Shiffeldrim, Hin H Gan, Tamar Schlick
    posted to pseudoknots rna structure by condon to the group beta on 2006-05-19 19:43:18 as ** along with 2 people and 2 groups marcius eckart_bindewald BioinfoCIPF SGU-CIPF
  • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.
    Nucleic Acids Res, Vol. 18, No. 10. (25 May 1990), pp. 3035-3044.
    by JP Abrahams, M van den Berg, E van Batenburg, C Pleij
    posted to pseudoknots rna structure by condon to the group beta on 2006-05-31 20:52:55 as ** along with 1 person guxiyou
  • Kissing of the two predominant hairpin loops in the coxsackie B virus 3' untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis
    J. Virol., Vol. 71, No. 1. (1 January 1997), pp. 686-696.
    by WJ Melchers, JG Hoenderop, Bruins, CW Pleij, EV Pilipenko, V Agol, JM Galama
    posted to pseudoknots rna structure by condon to the group beta on 2006-06-29 20:57:52 as ** along with 1 person Hosna
  • RNA loop-loop interactions as dynamic functional motifs
    Biochimie, Vol. 84, No. 9. (September 2002), pp. 925-944.
    by Christine Brunel, Roland Marquet, Pascale Romby, Chantal Ehresmann
    posted to pseudoknots by condon to the group beta on 2006-04-13 21:55:25 as *** along with 1 person austin
  • The language of RNA: a formal grammar that includes pseudoknots.
    Bioinformatics, Vol. 16, No. 4. (April 2000), pp. 334-340.
    by E Rivas, SR Eddy
    posted to pseudoknots rna structure by condon to the group beta on 2006-07-05 22:17:02 as ** along with 3 people evaf Hosna cthachuk
  • Pseudoknots: A Vital Feature in Viral RNA
    Seminars in Virology, Vol. 8, No. 3. (1997), pp. 166-175.
    by Birgit A Deiman, Cornelis W Pleij
    posted to pseudoknots review by condon to the group beta on 2006-06-29 20:43:56 as **
  • Topological constraints in nucleic acid hybridization kinetics.
    Nucleic Acids Res, Vol. 33, No. 13. (2005), pp. 4090-4095.
    by JS Bois, S Venkataraman, HM Choi, AJ Spakowitz, ZG Wang, NA Pierce
    posted to energy-model pseudoknots rna structure by condon to the group beta on 2006-05-18 01:29:49 as **
  • Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding.
    EMBO J, Vol. 17, No. 24. (15 December 1998), pp. 7498-7504.
    by MH Kolk, M van der Graaf, CT Fransen, SS Wijmenga, CW Pleij, HA Heus, CW Hilbers
    posted to pseudoknots rna by condon to the group beta on 2006-06-30 16:17:40 as **
  • Thermodynamics of folding a pseudoknotted mRNA fragment.
    J Mol Biol, Vol. 241, No. 2. (12 August 1994), pp. 246-262.
    by TC Gluick, DE Draper
    posted to folding-pathways pseudoknots rna structure by condon to the group beta on 2006-05-19 19:23:36 as **
  • The computer simulation of RNA folding involving pseudoknot formation.
    Nucleic Acids Res, Vol. 19, No. 9. (11 May 1991), pp. 2489-2494.
    by AP Gultyaev
    posted to pseudoknots rna structure by condon to the group beta on 2006-05-31 20:54:32 as **
  • NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.
    Science, Vol. 280, No. 5362. (17 April 1998), pp. 434-438.
    by MH Kolk, M van der Graaf, SS Wijmenga, CW Pleij, HA Heus, CW Hilbers
    posted to pseudoknots rna by condon to the group beta on 2006-06-30 18:37:38 as ** along with 1 person simone
  • tRNA-like structures. Structure, function and evolutionary significance.
    Eur J Biochem, Vol. 201, No. 2. (15 October 1991), pp. 303-324.
    by RM Mans, CW Pleij, L Bosch
    posted to pseudoknots rna by condon to the group beta on 2006-07-01 03:14:31 as **
  • A conformational switch at the 3' end of a plant virus RNA regulates viral replication.
    EMBO J, Vol. 18, No. 17. (1 September 1999), pp. 4856-4864.
    by RC Olsthoorn, S Mertens, FT Brederode, JF Bol
    posted to pseudoknots rna structure switch by condon to the group beta on 2006-07-01 03:19:24 as **
  • A new principle of RNA folding based on pseudoknotting
    Nucleic Acids Research, Vol. 13, No. 5. (11 March 1985), pp. 1717-1731.
    by CW Pleij, K Rietveld, L Bosch
    posted to pseudoknots rna by condon to the group beta on 2006-04-14 23:45:55 as **
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