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condon's rna [110 articles]

Recent papers added to condon's library classified by the tag rna. You can also see everyone's rna.
  • Predicting RNA pseudoknot folding thermodynamics
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2634-2652.
    by Song Cao, Shi J Chen
    posted to energy-model pseudoknot rna by condon on 2007-05-08 14:18:12 as ** along with 1 person and 1 group Kiarostami beta
  • 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 partition-function rna structure by condon on 2007-05-07 21:14:27 as ** along with 1 person and 1 group raylim beta
  • 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 rna structure tertiary by condon on 2007-03-23 23:50:17 as ** along with 1 group beta
  • 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 hierarchical rna structure tertiary by condon on 2007-03-23 23:22:31 as ** along with 1 group beta
  • 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 rna structure tertiary by condon on 2007-03-23 23:19:39 as ** along with 1 person and 1 group eckart_bindewald beta
  • 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 on 2007-01-29 15:37:09 as ** along with 1 group beta
  • 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 on 2006-11-11 18:19:54 as ** along with 2 people and 1 group mcox eckart_bindewald beta
  • 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 on 2006-10-31 21:49:48 as ** along with 4 people and 1 group Hosna apop physics Kiarostami beta
  • 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 on 2006-10-27 17:46:08 as ** along with 1 group beta
  • 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 on 2006-10-27 17:31:00 as ** along with 1 group beta
  • 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 on 2006-10-27 17:19:36 as ** along with 1 group beta
  • 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 on 2006-10-17 21:26:04 as ** along with 5 people and 3 groups evaf marcius arcticrasta Hosna Kiarostami beta 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 on 2006-08-17 20:37:30 as ** along with 3 people and 3 groups marcius eckart_bindewald arcticrasta beta 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 on 2006-08-17 20:35:41 as ** along with 6 people and 3 groups marcius arcticrasta penka Hosna physics Kiarostami beta 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 on 2006-08-17 20:33:41 as ** along with 1 person and 3 groups marcius beta 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 on 2006-08-17 19:46:39 as ** along with 6 people and 3 groups austin balajis marcius tardigrade penka acarbo beta 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 on 2006-07-14 23:43:50 as ** along with 1 group beta
  • 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 on 2006-07-13 21:03:31 as ** along with 1 group beta
  • 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 on 2006-07-13 19:54:21 as ** along with 1 group beta
  • 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 on 2006-07-13 19:32:24 as ** along with 1 person and 1 group Hosna beta
  • 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 on 2006-07-13 19:16:24 as ** along with 3 people and 5 groups marcius dchughes arcticrasta G4ID beta 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 on 2006-07-09 18:27:51 as ** along with 1 person and 1 group ruudvanleeuwen beta
  • 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 on 2006-07-09 18:26:24 as ** along with 1 person and 3 groups marcius beta 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 on 2006-07-09 18:21:21 as ** along with 1 person and 3 groups marcius beta 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 on 2006-07-09 18:17:04 as ** along with 4 people and 3 groups evaf marcius Hosna raylim beta 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 on 2006-07-09 18:11:55 as ** along with 1 person and 3 groups marcius beta 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 on 2006-07-09 18:00:17 as ** along with 1 person and 3 groups marcius beta 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 on 2006-07-09 17:57:20 as ** along with 3 people and 4 groups marcius penka i000 beta 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 on 2006-07-09 17:38:25 as ** along with 1 person and 3 groups marcius beta 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 on 2006-07-09 16:47:28 as ** along with 1 group beta
  • 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
  • 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 on 2006-07-02 19:21:50 as ** along with 3 people and 3 groups reyez marcius debatebob beta 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 on 2006-07-02 04:35:17 as ** along with 2 people and 1 group Hosna physics beta
  • Algorithms for the prediction of 3D RNA molecules
    (1998)
    by Alexander Renner
    posted to precition rna tertiary by condon on 2006-07-02 04:32:39 as ** along with 1 group beta
  • 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 on 2006-07-02 04:24:17 as ** along with 1 person and 1 group debatebob beta
  • 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 on 2006-07-02 04:03:56 as ** along with 3 people and 3 groups marcius j3xucite emidio_capriotti beta 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 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
  • 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 on 2006-07-01 05:16:02 as ** along with 22 people and 4 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 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
  • 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 on 2006-07-01 04:55:17 as ** along with 1 group beta
  • 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 on 2006-07-01 04:54:32 as ** along with 1 group beta
  • The Ribonuclease P Database
    Nucl. Acids Res., Vol. 27, No. 1. (1 January 1999), 314.
    by Jw Brown
    posted to database rna by condon on 2006-07-01 04:53:30 as ** along with 2 people and 1 group arcticrasta Hosna beta
  • 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 on 2006-07-01 04:51:48 as ** along with 1 person and 1 group vwchan beta
  • 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 on 2006-07-01 04:51:16 as ** along with 3 people and 3 groups marcius blackbart debatebob beta 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 on 2006-07-01 04:50:32 as ** along with 2 people and 1 group emidio_capriotti medic0747 beta
  • 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 on 2006-07-01 04:49:58 as ** along with 1 person and 1 group evaf 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 database rna by condon on 2006-07-01 04:46:35 as ** along with 3 people and 3 groups marcius arcticrasta Hosna beta BioinfoCIPF SGU-CIPF
  • 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 on 2006-07-01 04:34:42 as ** along with 2 people and 1 group evaf Hosna beta
  • 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 on 2006-07-01 04:33:53 as ** along with 1 person and 1 group Hosna beta
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