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Group: beta - with tag rna [114 articles]

Recent papers posted by members of the beta group with tag rna
  • A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
    BMC Bioinformatics, Vol. 3, No. 1. (2 July 2002)
    by SR Eddy
    posted to rna covariance by vwchan to the group beta on 2007-05-29 22:58:37 as ** along with 3 people and 2 groups evaf marcius mtagaya BioinfoCIPF SGU-CIPF
  • Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e56.
    by Eric P Nawrocki, Sean R Eddy
    posted to rna covariance by vwchan to the group beta on 2007-05-23 09:42:12 as **
  • Predicting RNA pseudoknot folding thermodynamics
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2634-2652.
    by Song Cao, Shi J Chen
    posted to rna pseudoknot energy-model by condon to the group beta on 2007-05-08 14:18:12 as ** along with 1 person Kiarostami
  • 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
  • A method for aligning RNA secondary structures and its application to RNA motif detection.
    BMC Bioinformatics, Vol. 6 (2005)
    by J Liu, JT Wang, J Hu, B Tian
    posted to rna alignment by vwchan to the group beta on 2007-02-01 12:38:57 as ** along with 2 people arcticrasta emidio_capriotti
  • A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. 4912-4924.
    by Lu, Zhi John, Turner, H Douglas, Mathews, H David
    posted to rna energy-parameters by condon to the group beta on 2007-01-29 15:37:09 as **
  • Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.
    Nucleic Acids Res, Vol. 8, No. 10. (24 May 1980), pp. 2275-2293.
    by CR Woese, LJ Magrum, R Gupta, RB Siegel, DA Stahl, J Kop, N Crawford, J Brosius, R Gutell, JJ Hogan, HF Noller
    posted to classic comparative rna by condon to the group beta on 2006-11-11 18:19:54 as ** along with 2 people mcox eckart_bindewald
  • Predicting RNA pseudoknot folding thermodynamics
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2634-2652.
    by Song Cao, Shi-Jie Chen
    posted to energy-model pseudoknot rna by condon to the group beta on 2006-10-31 21:49:48 as ** along with 4 people Hosna apop physics Kiarostami
  • RNA Structure Prediction Including Pseudoknots Based on Stochastic Multiple Context-Free Grammar
    Workshop on Probabilistic Modeling and Machine Learning in Structural and Systems Biology (2006)
    by Yuki Kato, Hiroyuki Seki, Tadao Kasami
    posted to rna tags by condon to the group beta on 2006-10-27 17:46:08 as **
  • Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
    Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE (2004), pp. 290-299.
    by H Matsui, K Sato, Y Sakakibara
    posted to rna tags by condon to the group beta on 2006-10-27 17:31:00 as **
  • 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 **
  • The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
    Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119.
    by JS McCaskill
    posted to rna by condon to the group beta on 2006-10-17 21:26:04 as ** along with 5 people and 2 groups evaf marcius arcticrasta Hosna Kiarostami BioinfoCIPF SGU-CIPF
  • 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 Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods
    Genetics, Vol. 157, No. 1. (1 January 2001), pp. 399-411.
    by Nicholas J Savill, David C Hoyle, Paul G Higgs
    posted to phylogeny-model rna by condon to the group beta on 2006-07-09 17:57:20 as ** along with 3 people and 3 groups marcius penka i000 BioinfoCIPF SGU-CIPF YY1
  • 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
  • SCOR: Structural Classification of RNA, version 2.0.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by M Tamura, DK Hendrix, PS Klosterman, NR Schimmelman, SE Brenner, SR Holbrook
    posted to database rna tertiary by condon to the group beta on 2006-07-02 19:21:50 as ** along with 3 people and 2 groups reyez marcius debatebob BioinfoCIPF SGU-CIPF
  • 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 to the group beta on 2006-07-02 04:35:17 as ** along with 2 people Hosna physics
  • Algorithms for the prediction of 3D RNA molecules
    (1998)
    by Alexander Renner
    posted to precition rna tertiary by condon to the group beta on 2006-07-02 04:32:39 as **
  • Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs.
    Nucleic Acids Res, Vol. 33, No. 4. (2005), pp. 1384-1398.
    by S Pasquali, HH Gan, T Schlick
    posted to design rna tertiary by condon to the group beta on 2006-07-02 04:24:17 as ** along with 1 person debatebob
  • RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
    Nucleic Acids Res, Vol. 31, No. 16. (15 August 2003), pp. 4755-4761.
    by CM Duarte, LM Wadley, AM Pyle
    posted to prediction rna tertiary by condon to the group beta on 2006-07-02 04:03:56 as ** along with 3 people and 2 groups marcius j3xucite emidio_capriotti BioinfoCIPF SGU-CIPF
  • 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 **
  • 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
  • The Protein Data Bank.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242.
    by HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne
    posted to database rna by condon to the group beta on 2006-07-01 05:16:02 as ** along with 22 people and 3 groups sebk higueruelo boris_aguilar nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso leelarcombe aengisch debatebob massivemayhem gisle girschick selrac tji Radiation_Damage Stressosome biomedical-nlp
  • 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
  • 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 **
  • tmRDB (tmRNA database).
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 446-447.
    by C Zwieb, J Gorodkin, B Knudsen, J Burks, J Wower
    posted to database rna by condon to the group beta on 2006-07-01 04:54:32 as **
  • The Ribonuclease P Database
    Nucl. Acids Res., Vol. 27, No. 1. (1 January 1999), 314.
    by Jw Brown
    posted to database rna by condon to the group beta on 2006-07-01 04:53:30 as ** along with 2 people arcticrasta Hosna
  • Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by M Sprinzl, KS Vassilenko
    posted to database rna by condon to the group beta on 2006-07-01 04:51:48 as ** along with 1 person vwchan
  • RNABase: an annotated database of RNA structures.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 502-504.
    by VL Murthy, GD Rose
    posted to database rna by condon to the group beta on 2006-07-01 04:51:16 as ** along with 3 people and 2 groups marcius blackbart debatebob BioinfoCIPF SGU-CIPF
  • The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.
    Biophys J, Vol. 63, No. 3. (September 1992), pp. 751-759.
    by HM Berman, WK Olson, DL Beveridge, J Westbrook, A Gelbin, T Demeny, SH Hsieh, AR Srinivasan, B Schneider
    posted to database rna by condon to the group beta on 2006-07-01 04:50:32 as ** along with 2 people emidio_capriotti medic0747
  • The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
    BMC Bioinformatics, Vol. 3, No. 1. (2002)
    by JJ Cannone, S Subramanian, MN Schnare, JR Collett, LM D'Souza, Y Du, B Feng, N Lin, LV Madabusi, KM Müller, N Pande, Z Shang, N Yu, RR Gutell
    posted to database rna by condon to the group beta on 2006-07-01 04:49:58 as ** along with 1 person evaf
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