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condon's pseudoknots [32 articles]

Recent papers added to condon's library classified by the tag pseudoknots. You can also see everyone's pseudoknots.
  • KnotSeeker: Heuristic pseudoknot detection in long RNA sequences
    RNA, Vol. 14, No. 4. (1 April 2008), pp. 630-640.
    by Jana Sperschneider, Amitava Datta
    posted to pseudoknots by condon on 2008-03-26 20:41:57 as ** along with 2 people Hosna physics
  • 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 on 2006-07-05 22:17:02 as ** along with 3 people and 1 group evaf Hosna cthachuk 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 rna tertiary by condon on 2006-07-02 04:35:17 as ** along with 2 people and 1 group Hosna physics beta
  • 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 on 2006-07-02 03:51:54 as ** along with 1 group beta
  • Programmed ribosomal frameshifting: Much ado about knotting!
    PNAS, Vol. 96, No. 25. (7 December 1999), pp. 14177-14179.
    by SL Alam, JF Atkins, RF Gesteland
    posted to pseudoknots review rna structure by condon on 2006-07-01 16:36:02 as ** along with 1 person and 1 group Hosna beta
  • 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 on 2006-07-01 05:10:44 as ** along with 9 people and 1 group evaf balajis eckart_bindewald arcticrasta dquest Hosna jarasch physics guxiyou beta
  • 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 on 2006-07-01 03:38:27 as ** along with 1 person and 1 group Hosna beta
  • 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 on 2006-07-01 03:19:24 as ** along with 1 group beta
  • 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 on 2006-07-01 03:14:31 as ** along with 1 group beta
  • 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 on 2006-06-30 18:37:38 as ** along with 1 person and 1 group simone beta
  • 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 on 2006-06-30 16:17:40 as ** along with 1 group beta
  • 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 on 2006-06-29 20:57:52 as ** along with 1 person and 1 group Hosna beta
  • A Phylogenetically Conserved Hairpin-Type 3' Untranslated Region Pseudoknot Functions in Coronavirus RNA Replication
    J. Virol., Vol. 73, No. 10. (1 October 1999), pp. 8349-8355.
    by Gwyn D Williams, Ruey-Yi Chang, David A Brian
    posted to pseudoknots rna structure by condon on 2006-06-29 20:51:58 as ** along with 1 group beta
  • 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 on 2006-06-29 20:43:56 as ** along with 1 group beta
  • 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 on 2006-06-29 20:35:53 as ** along with 1 group beta
  • 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 on 2006-05-31 20:58:36 as ** along with 2 people and 1 group Hosna guxiyou beta
  • 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 on 2006-05-31 20:54:32 as ** along with 1 group beta
  • 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 on 2006-05-31 20:52:55 as ** along with 1 person and 1 group guxiyou beta
  • RNA pseudoknot prediction in energy-based models.
    J Comput Biol, Vol. 7, No. 3-4. (2000), pp. 409-427.
    by RB Lyngso, CN Pedersen
    posted to np pseudoknots rna structure by condon on 2006-05-19 19:52:56 as ** along with 4 people and 1 group evaf arcticrasta Hosna guxiyou beta
  • 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 on 2006-05-19 19:43:18 as ** along with 2 people and 3 groups marcius eckart_bindewald beta BioinfoCIPF SGU-CIPF
  • 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 on 2006-05-19 19:23:36 as ** along with 1 group beta
  • Complexity of Pseudoknot Prediction in Simple Models
    Vol. 3142 (January 2004), pp. 919-931.
    by Rune B Lyngso
    edited by Josep Diaz, Juhani Karhumäki, Arto Lepistö, Donald Sannella
    posted to np pseudoknots rna by condon on 2006-05-19 19:07:16 as ** along with 1 group beta
  • 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 pseudoknots rna structure by condon on 2006-05-18 18:57:29 as ** along with 3 people and 1 group Hosna Kiarostami guxiyou beta
  • 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 on 2006-05-18 18:48:12 as ** along with 1 person and 1 group Hosna beta
  • 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 on 2006-05-18 01:47:52 as ** along with 4 people and 3 groups marcius eckart_bindewald arcticrasta Hosna beta BioinfoCIPF SGU-CIPF
  • 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 on 2006-05-18 01:29:49 as ** along with 1 group beta
  • 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 on 2006-05-15 22:19:00 as ** along with 4 people and 3 groups austin marcius arcticrasta Hosna beta BioinfoCIPF SGU-CIPF
  • New catalytic structures from an existing ribozyme
    Nature Structural & Molecular Biology, Vol. 12, No. 11. (09 October 2005), pp. 994-1000.
    by Edward A Curtis, David P Bartel
    posted to pseudoknots rna structure by condon on 2006-05-15 22:10:32 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • 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 on 2006-04-14 23:59:21 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • 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 on 2006-04-14 23:45:55 as ** along with 1 group beta
  • 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 folding pseudoknots rna by condon on 2006-04-14 00:01:16 as ** along with 6 people and 3 groups evaf austin marcius arcticrasta Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
  • 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 on 2006-04-13 21:55:25 as *** along with 1 person and 1 group austin beta
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