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Group: beta - with tag structure [65 articles]

Recent papers posted by members of the beta group with tag structure
  • Moments of the Boltzmann distribution for RNA secondary structures
    Bulletin of Mathematical Biology, Vol. 67, No. 5. (2005), pp. 1031-1047.
    by István Miklós, Irmtraud M Meyer, Borbála Nagy
    posted to structure rna partition-function by condon to the group beta on 2007-05-07 21:14:27 as ** along with 1 person raylim
  • G-ribo: A new structural motif in ribosomal RNA
    RNA, Vol. 13, No. 4. (1 April 2007), pp. 549-554.
    by Sergey V Steinberg, Yury I Boutorine
    posted to tertiary structure rna by condon to the group beta on 2007-03-23 23:50:17 as **
  • RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts.
    J Am Chem Soc, Vol. 127, No. 13. (6 April 2005), pp. 4659-4667.
    by KA Wilkinson, EJ Merino, KM Weeks
    posted to tertiary structure rna hierarchical by condon to the group beta on 2007-03-23 23:22:31 as **
  • RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).
    J Am Chem Soc, Vol. 127, No. 12. (30 March 2005), pp. 4223-4231.
    by EJ Merino, KA Wilkinson, JL Coughlan, KM Weeks
    posted to tertiary structure rna by condon to the group beta on 2007-03-23 23:19:39 as ** along with 1 person eckart_bindewald
  • Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing.
    Antisense Nucleic Acid Drug Dev, Vol. 13, No. 2. (April 2003), pp. 83-105.
    by J Harborth, SM Elbashir, K Vandenburgh, H Manninga, SA Scaringe, K Weber, T Tuschl
    posted to review rna structure by condon to the group beta on 2006-10-27 17:19:36 as **
  • A bayesian statistical algorithm for RNA secondary structure prediction.
    Comput Chem, Vol. 23, No. 3-4. (15 June 1999), pp. 387-400.
    by Y Ding, CE Lawrence
    posted to prediction rna structure by condon to the group beta on 2006-08-17 20:37:30 as ** along with 3 people and 2 groups marcius eckart_bindewald arcticrasta BioinfoCIPF SGU-CIPF
  • Statistical and Bayesian approaches to RNA secondary structure prediction.
    RNA, Vol. 12, No. 3. (March 2006), pp. 323-331.
    by Y Ding
    posted to review rna structure by condon to the group beta on 2006-08-17 20:35:41 as ** along with 6 people and 2 groups marcius arcticrasta penka Hosna physics Kiarostami BioinfoCIPF SGU-CIPF
  • Extracting stacking interaction parameters for RNA from the data set of native structures.
    J Mol Biol, Vol. 347, No. 1. (18 March 2005), pp. 53-69.
    by RI Dima, C Hyeon, D Thirumalai
    posted to energy-model rna structure by condon to the group beta on 2006-08-17 20:33:41 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • CONTRAfold: RNA secondary structure prediction without physics-based models.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by CB Do, DA Woods, S Batzoglou
    posted to rna scfgs structure by condon to the group beta on 2006-08-17 19:46:39 as ** along with 6 people and 2 groups austin balajis marcius tardigrade penka acarbo BioinfoCIPF SGU-CIPF
  • Efficient Algorithm for RNA Pseudoknotted Secondary Structure Prediction Given a Pseudoknot Free Structure
    (2005)
    by YS Zhao
    posted to hierarchical rna structure by condon to the group beta on 2006-07-14 23:43:50 as **
  • New insight into RNase P RNA structure from comparative analysis of the archaeal RNA.
    RNA, Vol. 7, No. 2. (February 2001), pp. 220-232.
    by JK Harris, ES Haas, D Williams, DN Frank, JW Brown
    posted to rna structure by condon to the group beta on 2006-07-13 21:03:31 as **
  • Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot
    Journal of Molecular Biology, Vol. 270, No. 3. (18 July 1997), pp. 451-463.
    by Thomas C Gluick, Resi B Gerstner, David E Draper
    posted to experimental folding-pathways rna structure by condon to the group beta on 2006-07-13 19:54:21 as **
  • 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 experimental rna structure by condon to the group beta on 2006-07-13 19:32:24 as ** along with 1 person Hosna
  • Structural genomics of RNA.
    Nat Struct Biol, Vol. 7 Suppl (November 2000), pp. 954-956.
    by JA Doudna
    posted to review rna structure by condon to the group beta on 2006-07-13 19:16:24 as ** along with 3 people and 4 groups marcius dchughes arcticrasta G4ID BioinfoCIPF SGU-CIPF Genetics-of-Gambling
  • Probing the Mechanical Folding Kinetics of TAR RNA by Hopping, Force-Jump, and Force-Ramp Methods
    Biophys. J., Vol. 90, No. 1. (1 January 2006), pp. 250-260.
    by Pan T Li, Delphine Collin, Steven B Smith, Carlos Bustamante, Ignacio Tinoco
    posted to folding-pathways rna structure by condon to the group beta on 2006-07-09 18:27:51 as ** along with 1 person ruudvanleeuwen
  • Strategies for RNA folding and assembly.
    Nat Rev Mol Cell Biol, Vol. 5, No. 11. (November 2004), pp. 908-919.
    by R Schroeder, A Barta, K Semrad
    posted to folding-pathways review rna structure by condon to the group beta on 2006-07-09 18:26:24 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Native secondary structure formation in RNA may be a slave to tertiary folding
    PNAS, Vol. 95, No. 20. (29 September 1998), pp. 11506-11508.
    by D Thirumalai
    posted to review rna structure tertiary by condon to the group beta on 2006-07-09 18:21:21 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Co-transcriptional folding is encoded within RNA genes.
    BMC Mol Biol, Vol. 5, No. 1. (6 August 2004)
    by IM Meyer, I Miklós
    posted to co-transcriptional-folding rna structure by condon to the group beta on 2006-07-09 18:17:04 as ** along with 4 people and 2 groups evaf marcius Hosna raylim BioinfoCIPF SGU-CIPF
  • Overlaps between RNA secondary structures.
    PHYSICAL REVIEW LETTERS, Vol. 76, No. 4. (22 January 1996), pp. 704-707.
    by PG Higgs
    posted to energy-landscapes rna structure by condon to the group beta on 2006-07-09 18:11:55 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Comparative sequence analysis of tmRNA.
    Nucleic Acids Res, Vol. 27, No. 10. (15 May 1999), pp. 2063-2071.
    by C Zwieb, I Wower, J Wower
    posted to rna structure by condon to the group beta on 2006-07-09 18:00:17 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • RNA backbone is rotameric.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 13904-13909.
    by LJ Murray, WB Arendall, DC Richardson, JS Richardson
    posted to computational-experimental rna structure tertiary by condon to the group beta on 2006-07-09 17:38:25 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Methods for refining interactively established models of ribosomal RNA towards a physico-chemically plausible structure
    Journal of Computational Chemistry, Vol. 22, No. 4. (2001), pp. 407-417.
    by Ingolf Sommer, Richard Brimacombe
    posted to computational-experimental rna structure tertiary by condon to the group beta on 2006-07-09 16:47:28 as **
  • 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
  • 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 to the group beta on 2006-07-01 16:36:02 as ** along with 1 person Hosna
  • PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3432-3440.
    by K Han, Y Byun
    posted to rna structure visualization by condon to the group beta on 2006-07-01 04:55:17 as **
  • A partition function algorithm for nucleic acid secondary structure including pseudoknots.
    J Comput Chem, Vol. 24, No. 13. (October 2003), pp. 1664-1677.
    by RM Dirks, NA Pierce
    posted to partition rna structure by condon to the group beta on 2006-07-01 04:34:42 as ** along with 2 people evaf Hosna
  • The brave new world of RNA.
    Nature, Vol. 418, No. 6894. (11 July 2002), pp. 122-124.
    by C Dennis
    posted to review rna structure by condon to the group beta on 2006-07-01 04:33:53 as ** along with 1 person Hosna
  • 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 **
  • The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution.
    EMBO J, Vol. 16, No. 12. (16 June 1997), pp. 3685-3692.
    by MH Kolk, HA Heus, CW Hilbers
    posted to rna structure by condon to the group beta on 2006-06-30 18:40:21 as **
  • 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
  • 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 to the group beta on 2006-06-29 20:51:58 as **
  • RNA Structure and Stability
    Seminars in Virology, Vol. 8, No. 3. (1997), pp. 153-165.
    by Jacek Nowakowski, Jr Tinoco
    posted to energy-model review rna structure by condon to the group beta on 2006-06-29 20:32:22 as **
  • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
    RNA, Vol. 10, No. 8. (August 2004), pp. 1178-1190.
    by DH Mathews
    posted to rna structure by condon to the group beta on 2006-06-09 22:58:17 as ** along with 5 people austin evaf arcticrasta Hosna Kiarostami
  • 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 2 people Hosna guxiyou
  • 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 **
  • 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
  • Energy directed folding of RNA sequences.
    Nucleic Acids Res, Vol. 12, No. 1 Pt 1. (11 January 1984), pp. 67-74.
    by P Hogeweg, B Hesper
    posted to rna structure by condon to the group beta on 2006-05-30 18:35:41 as **
  • Predicting RNA secondary structure by free energy minimization
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) (May 2006), pp. 1-9.
    by David Mathews
    posted to hierarchical-model prediction review rna structure by condon to the group beta on 2006-05-19 20:10:29 as ** along with 5 people and 2 groups marcius Hosna hesam cthachuk apop BioinfoCIPF SGU-CIPF
  • 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 to the group beta on 2006-05-19 19:52:56 as ** along with 4 people evaf arcticrasta Hosna guxiyou
  • 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
  • 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 **
  • Isolation of high-affinity GTP aptamers from partially structured RNA libraries
    PNAS, Vol. 99, No. 18. (3 September 2002), pp. 11616-11621.
    by Jonathan H Davis, Jack W Szostak
    posted to in-vitro-selection rna structure by condon to the group beta on 2006-05-19 19:05:50 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 pseudoknots rna structure by condon to the group beta on 2006-05-18 18:57:29 as ** along with 3 people Hosna Kiarostami guxiyou
  • 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
  • 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 database rna structure by condon to the group beta on 2006-05-18 18:35:44 as ** along with 1 person Hosna
  • Fast evaluation of internal loops in RNA secondary structure prediction
    Bioinformatics, Vol. 15, No. 6. (1 June 1999), pp. 440-445.
    by Rb Lyngso, M Zuker, Cn Pedersen
    posted to rna structure by condon to the group beta on 2006-05-18 18:33:25 as ** along with 2 people and 2 groups marcius arcticrasta BioinfoCIPF SGU-CIPF
  • Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures.
    Nucleic Acids Res, Vol. 31, No. 7. (1 April 2003), pp. 2006-2013.
    by J Kitagawa, Y Futamura, K Yamamoto
    posted to energy-landscapes rna structure by condon to the group beta on 2006-05-18 18:31:10 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
  • 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 **
  • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
    J Mol Biol, Vol. 288, No. 5. (21 May 1999), pp. 911-940.
    by DH Mathews, J Sabina, M Zuker, DH Turner
    posted to energy-model rna structure by condon to the group beta on 2006-05-18 00:34:37 as ** along with 2 people evaf zahra
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