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austin's folding [35 articles]

Recent papers added to austin's library classified by the tag folding. You can also see everyone's folding.
  • Structural specificity conferred by a group I RNA peripheral element.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 29. (19 July 2005), pp. 10176-10181.
    by TH Johnson, P Tijerina, AB Chadee, D Herschlag, R Russell
    posted to biochemistry folding tetrahymena by austin on 2008-08-24 02:32:48 as read
  • Folding problems of the 5' splice site containing the P1 stem of the group I thymidylate synthase intron: substrate binding inhibition in vitro and mis-splicing in vivo.
    The Journal of biological chemistry, Vol. 277, No. 20. (17 May 2002), pp. 17987-17993.
    by A Pichler, R Schroeder
    posted to biochemistry folding groupi ribozyme by austin on 2008-08-22 20:49:22 as read
  • The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core.
    Biochemistry, Vol. 36, No. 11. (18 March 1997), pp. 3159-3169.
    by EA Doherty, JA Doudna
    posted to folding tetrahymena by austin on 2008-08-17 03:34:26 as read
  • Intracellular folding of the Tetrahymena group I intron depends on exon sequence and promoter choice.
    RNA (New York, N.Y.), Vol. 10, No. 10. (October 2004), pp. 1526-1532.
    by SP Koduvayur, SA Woodson
    posted to biochemistry folding tetrahymena by austin on 2008-08-17 03:29:30 as read
  • Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast.
    RNA (New York, N.Y.), Vol. 12, No. 12. (December 2006), pp. 2149-2159.
    by SA Jackson, S Koduvayur, SA Woodson
    posted to folding groupi kinetictrap rna tetrahymena by austin on 2008-07-21 04:10:19 as read
  • notes Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme.
    Biochemistry, Vol. 46, No. 17. (1 May 2007), pp. 4951-4961.
    by R Russell, P Tijerina, AB Chadee, H Bhaskaran
    posted to folding kinetictrap ribozyme tetrahymena by austin on 2008-07-20 01:51:43 as read
  • 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 folding prediction rna secondary structure by austin on 2008-07-17 02:09:45 as read along with 6 people and 3 groups balajis marcius tardigrade penka condon acarbo beta BioinfoCIPF SGU-CIPF
  • One sequence, two ribozymes: implications for the emergence of new ribozyme folds
    Science, Vol. 289, No. 5478. (21 July 2000), pp. 448-452.
    by Erik A Schultes, David P Bartel
    posted to folding ligase ribozyme syntheticbiology by austin on 2008-07-16 00:23:59 as read along with 3 people and 3 groups marcius condon Hosna beta BioinfoCIPF SGU-CIPF
  • RNA folding: models and perspectives.
    Curr Opin Struct Biol, Vol. 13, No. 3. (June 2003), pp. 309-316.
    by TR Sosnick, T Pan
    posted to folding rna by austin on 2008-07-04 23:59:38 as read along with 3 people and 2 groups evaf marcius Hosna BioinfoCIPF SGU-CIPF
  • Prediction of RNA secondary structure by free energy minimization.
    Curr Opin Struct Biol, Vol. 16, No. 3. (June 2006), pp. 270-278.
    by DH Mathews, DH Turner
    posted to folding rna by austin on 2008-07-04 23:58:34 as ** along with 1 person onufriev
  • Predicting a set of minimal free energy RNA secondary structures common to two sequences.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2246-2253.
    by DH Mathews
    posted to folding rna by austin on 2008-07-04 23:58:21 as read along with 3 people and 2 groups marcius eckart_bindewald arcticrasta BioinfoCIPF SGU-CIPF
  • 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 folding rna by austin on 2008-07-04 23:58:02 as read along with 5 people and 1 group evaf arcticrasta condon Hosna Kiarostami beta
  • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
    Proc Natl Acad Sci U S A, Vol. 101, No. 19. (11 May 2004), pp. 7287-7292.
    by DH Mathews, MD Disney, JL Childs, SJ Schroeder, M Zuker, DH Turner
    posted to folding rna by austin on 2008-07-04 23:57:43 as read along with 4 people and 1 group eckart_bindewald arcticrasta condon Hosna beta
  • A method for rapid similarity analysis of RNA secondary structures
    BMC Bioinformatics, Vol. 7 (08 November 2006), 493.
    by Na Liu, Tianming Wang
    posted to folding rna by austin on 2008-07-04 23:57:22 as read along with 1 person dquest
  • How do RNA folding algorithms work?
    Nature Biotechnology, Vol. 22, No. 11., 1457.
    by Sean R Eddy
    posted to folding rna by austin on 2008-07-04 23:56:18 as read along with 10 people and 2 groups evaf marcius tardigrade mtagaya 3times3 cthachuk magnolia maralena guxiyou cambray BioinfoCIPF SGU-CIPF
  • RNA folding during transcription.
    Annual review of biophysics and biomolecular structure, Vol. 35 (2006), pp. 161-175.
    by T Pan, T Sosnick
    posted to folding ribozyme rna transcription by austin on 2008-07-04 14:00:08 as **
  • RNA folding causes secondary structure rearrangement.
    Proc Natl Acad Sci U S A, Vol. 95, No. 20. (29 September 1998), pp. 11555-11560.
    by M Wu, I Tinoco
    posted to folding groupi tetrahymena by austin on 2008-07-03 14:27:09 as read along with 4 people and 3 groups marcius condon Hosna apop beta BioinfoCIPF SGU-CIPF
  • Kinetic intermediates trapped by native interactions in RNA folding
    Science, Vol. 279, No. 5358. (20 March 1998), pp. 1943-1946.
    by Daniel K Treiber, Martha S Rook, Patrick P Zarrinkar, James R Williamson
    posted to folding rna tetrahymena by austin on 2008-06-25 22:52:09 as read
  • Folding intermediates of a self-splicing RNA: mispairing of the catalytic core.
    Journal of molecular biology, Vol. 280, No. 4. (24 July 1998), pp. 597-609.
    by J Pan, SA Woodson
    posted to folding groupi ribozyme rna tetrahymena by austin on 2008-06-25 21:57:52 as read
  • Tertiary interactions determine the accuracy of RNA folding.
    Journal of the American Chemical Society, Vol. 130, No. 4. (30 January 2008), pp. 1296-1303.
    by S Chauhan, SA Woodson
    posted to folding structure tetrahymena by austin on 2008-06-17 03:53:37 as read
  • Recent insights on RNA folding mechanisms from catalytic RNA.
    Cellular and molecular life sciences : CMLS, Vol. 57, No. 5. (May 2000), pp. 796-808.
    by SA Woodson
    posted to folding ribozyme rna by austin on 2008-06-02 20:59:53 as **
  • Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway.
    Journal of molecular biology, Vol. 308, No. 5. (18 May 2001), pp. 839-851.
    by R Russell, D Herschlag
    posted to folding kinetictrap ribozyme tetrahymena by austin on 2008-06-02 20:58:31 as *****
  • Kinetic intermediates in RNA folding.
    Science (New York, N.Y.), Vol. 265, No. 5174. (12 August 1994), pp. 918-924.
    by PP Zarrinkar, JR Williamson
    posted to folding ribozyme tetrayhmena by austin on 2008-06-02 20:55:15 as *****
  • RNA chaperones, RNA annealers and RNA helicases.
    RNA biology, Vol. 4, No. 3. (November 2007), pp. 118-130.
    by L Rajkowitsch, D Chen, S Stampfl, K Semrad, C Waldsich, O Mayer, MF Jantsch, R Konrat, U Bläsi, R Schroeder
    posted to annealing chaperone folding helicase review rna by austin on 2008-05-29 17:13:19 as read
  • Evidence for kinetic effects in the folding of large RNA molecules
    The Journal of Chemical Physics, Vol. 105, No. 16. (1996), pp. 7152-7157.
    by Steven R Morgan, Paul G Higgs
    posted to folding kinetics rna by austin on 2008-05-25 18:25:00 as read
  • Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors
    Nucl. Acids Res. (23 December 2007), gkm1048.
    by Cody Geary, Stephanie Baudrey, Luc Jaeger
    posted to folding gnra rna tetraloop by austin on 2008-05-11 21:34:27 as read
  • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    Nature, Vol. 452, No. 7183. (2008), pp. 51-55.
    by Marc Parisien, François Major
    posted to folding prediction rna software structure by austin on 2008-05-10 17:34:39 as read along with 4 people puranjoy_b zwang elfar reyez
  • RNA folding at elementary step resolution.
    RNA, Vol. 6, No. 3. (March 2000), pp. 325-338.
    by C Flamm, W Fontana, IL Hofacker, P Schuster
    posted to folding kinetics kinfold rna by austin on 2008-04-15 16:44:38 as read along with 4 people arcticrasta ilh mtw Kiarostami
  • 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 folding kinefold kinetics pseudoknot rna by austin on 2008-04-15 15:48:23 as read along with 3 people eckart_bindewald Hosna Kiarostami
  • Encoding folding paths of RNA switches.
    Nucleic acids research, Vol. 35, No. 2. (2007), pp. 614-622.
    by A Xayaphoummine, V Viasnoff, S Harlepp, H Isambert
    posted to design folding kinefold rna switch by austin on 2008-04-15 14:31:47 as read
  • Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
    Science (3 January 2008), 1151298.
    by William J Greenleaf, Kirsten L Frieda, Daniel A Foster, Michael T Woodside, Steven M Block
    posted to folding rna by austin on 2008-01-10 04:04:03 as read along with 2 people jvf666 paulschlesinger
  • A new principle of RNA folding based on pseudoknotting.
    Nucleic Acids Res, Vol. 13, No. 5. (11 March 1985), pp. 1717-1731.
    by CW Pleij, K Rietveld, L Bosch
    posted to folding pseudoknot rna by austin on 2007-08-28 20:27:56 as read
  • ILM: a web server for predicting RNA secondary structures with pseudoknots.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by J Ruan, GD Stormo, W Zhang
    posted to folding prediction pseudoknot rna website by austin on 2007-08-27 14:35:42 as read along with 1 person balajis
  • pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by J Reeder, P Steffen, R Giegerich
    posted to folding pesudoknot rna useful website by austin on 2007-08-26 22:02:54 as read
  • INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by A Busch, R Backofen
    posted to folding inverse rna website by austin on 2007-08-26 21:47:51 as read
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