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Ключевое слово pseudoknot [42 articles]

Recent papers classified by the tag pseudoknot.
  • Fast and Accurate Search for Non-coding RNA Pseudoknot Structures in Genomes.
    Bioinformatics (Oxford, England) (7 August 2008)
    by Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L L Malmberg, Liming Cai
    posted to structure rna pseudoknot prediction by samgj on 2008-10-09 14:27:58 as ** along with 3 people djkt Ema papamicd
  • Predicting RNA pseudoknot folding thermodynamics
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2634-2652.
    by Cao, Song, Chen, Shi-Jie
    posted to biophysics prediction pseudoknot rna thermodynamics by physics on 2007-05-05 22:31:50 as *** along with 4 people and 1 group condon Hosna apop Kiarostami beta
  • Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
    RNA, Vol. 14, No. 6. (1 June 2008), pp. 1164-1173.
    by Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V Demidov, Natalia E Broude, Nikolay V Dokholyan
    posted to pseudoknot tertiary by physics on 2008-07-21 17:31:57 as *** along with 2 people carmaus Hosna
  • 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 pseudoknot thermodynamics by physics on 2007-05-07 03:35:28 as *** along with 2 people and 1 group condon 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 pseudoknot rna by physics on 2007-05-05 22:46:48 as *** along with 9 people and 1 group evaf balajis eckart_bindewald arcticrasta dquest condon Hosna jarasch guxiyou beta
  • 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 prediction pseudoknot by physics on 2008-03-23 16:06:01 as *** along with 2 people condon Hosna
  • Predicting ribosomal frameshifting efficiency
    Phys. Biol., Vol. 5, No. 1. (March 2008), 016002.
    by Song Cao, Shi-Jie Chen
    posted to force frameshifting pseudoknot by physics on 2008-03-23 15:57:54 as ***
  • Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity.
    J Mol Biol, Vol. 367, No. 3. (30 March 2007), pp. 909-924.
    by S Cao, SJ Chen
    posted to kinetics pseudoknot rna telomerase by physics on 2007-05-05 22:48:13 as ***
  • Novel and efficient RNA secondary structure prediction using hierarchical folding.
    J Comput Biol, Vol. 15, No. 2. (March 2008), pp. 139-163.
    by H Jabbari, A Condon, S Zhao
    posted to prediction pseudoknot rna by physics on 2008-03-24 05:21:05 as *** along with 2 people eskay Hosna
  • A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal
    PLoS Biology, Vol. 3, No. 6. (1 June 2005), e172.
    by Ewan P Plant, Gabriela C Pérez-Alvarado, Jonathan L Jacobs, Bani Mukhopadhyay, Mirko Hennig, Jonathan D Dinman
    posted to frameshifting pseudoknot by physics on 2008-03-29 06:04:36 as *** along with 1 person jonathanjacobs
  • A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting
    Nature, Vol. 441, No. 7090., pp. 244-247.
    by Olivier Namy, Stephen J Moran, David I Stuart, Robert JC Gilbert, Ian Brierley
    posted to force frameshifting pseudoknot by physics on 2007-05-05 22:34:13 as ***
  • Torsional restraint: a new twist on frameshifting pseudoknots
    Nucleic Acids Research, Vol. 33, No. 6. (2005), pp. 1825-1833.
    by Ewan P Plant, Jonathan D Dinman
    posted to frameshifting pseudoknot rna by physics on 2007-05-05 22:43:52 as ***
  • High sensitivity RNA pseudoknot prediction
    Nucleic Acids Research, Vol. 35, No. 2. (January 2007), pp. 656-663.
    by Huang, Xiaolu, Ali, Hesham
    posted to pseudoknot by physics on 2007-04-26 16:22:01 as ***
  • Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting
    PNAS, Vol. 104, No. 14. (3 April 2007), pp. 5830-5835.
    by Thomas M Hansen, Reihani, Lene B Oddershede, Michael A Sorensen
    posted to biophysics force frameshifting pseudoknot by physics on 2007-04-26 16:23:20 as *** along with 2 people lshaw jwagoner
  • The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
    RNA, Vol. 9, No. 2. (February 2003), pp. 168-174.
    by EP Plant, KL Jacobs, JW Harger, A Meskauskas, JL Jacobs, JL Baxter, AN Petrov, JD Dinman
    posted to force frameshifting pseudoknot by physics on 2007-05-05 22:53:49 as *** along with 2 people jonathanjacobs KristiMuldoonJacobs
  • Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by A Xayaphoummine, T Bucher, H Isambert
    posted to folding-pathways kinefold pseudoknot by Kiarostami on 2007-05-09 01:08:18 as ** along with 1 person austin
  • PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Ashton Belew, Nicholaus Hepler, Jonathan Jacobs, Jonathan Dinman
    posted to bioinformatics biology cerevisiae computational database decay frameshift genome mrna nmd pseudoknot rna saccharomyces structure translation virus yeast by jonathanjacobs on 2008-07-17 17:12:43 as read
  • Identification of functional, endogenous programmed 1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
    Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. 165-174.
    by Jacobs, L Jonathan, Belew, T Ashton, Rakauskaite, Rasa, Dinman, D Jonathan
    posted to genomics cerevisiae codon computational database frameshift laboratory mrna pathway protein pseudoknot ribosome saccharomyces statistics transcription translation virus yeast by jonathanjacobs on 2008-03-28 04:26:08 as read
  • Non-AUG-Initiated Internal Translation of the L* Protein of Theiler's Virus and Importance of This Protein for Viral Persistence
    J. Virol., Vol. 76, No. 21. (1 November 2002), pp. 10665-10673.
    by Olivier van Eyll, Thomas Michiels
    posted to multiple_sclerosis pseudoknot by Hosna on 2007-05-08 01:53:36 as **
  • The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases
    RNA, Vol. 12, No. 7. (1 July 2006), pp. 1149-1153.
    by Norma M Wills, John F Atkins
    posted to alzheimer pseudoknot by Hosna on 2007-05-08 01:14:12 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 pseudoknot rna by evaf on 2005-03-10 21:20:35 as ** along with 3 people and 1 group condon Hosna cthachuk beta
  • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.
    Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 58-66.
    by J Ruan, GD Stormo, W Zhang
    posted to pseudoknot rna by evaf on 2005-03-10 21:21:16 as ** along with 3 people and 1 group arcticrasta condon Hosna beta
  • Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching.
    Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 753-758.
    by I Barrette, G Poisson, P Gendron, F Major
    posted to prion pseudoknot rna by evaf on 2005-03-10 21:10:11 as **
  • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.
    J Comput Chem, Vol. 25, No. 10. (30 July 2004), pp. 1295-1304.
    by RM Dirks, NA Pierce
    posted to pseudoknot rna by evaf on 2005-03-10 21:11:59 as ** along with 2 people arcticrasta miyake
  • 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 pseudoknot rna secondary_structure by evaf on 2005-04-06 12:21:14 as *** along with 6 people and 3 groups austin marcius arcticrasta condon Hosna Kiarostami 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_function pseudoknot rna secondary_structure by evaf on 2005-03-10 21:11:55 as ** along with 2 people and 1 group condon Hosna beta
  • RNA pseudoknot prediction in energy-based models.
    J Comput Biol, Vol. 7, No. 3-4. (2000), pp. 409-427.
    by RB Lyngsø, CN Pedersen
    posted to pseudoknot rna by evaf on 2005-03-10 21:17:38 as ** along with 4 people and 1 group arcticrasta condon Hosna guxiyou beta
  • New developments in structure determination of pseudoknots
    Biopolymers, Vol. 48, No. 2-3. (1998), pp. 137-153.
    by Cornelis W Hilbers, Paul JA Michiels, Hans A Heus
    posted to pseudoknot review by eckart_bindewald on 2006-08-29 12:09:52 as ****
  • 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 monte_carlo pseudoknot rna by eckart_bindewald on 2006-08-29 16:02:38 as *** along with 3 people austin Hosna Kiarostami
  • Beyond Mfold: Recent advances in RNA bioinformatics.
    J Biotechnol (9 March 2006)
    by Jens Reeder, Matthias Höchsmann, Marc Rehmsmeier, Björn Voss, Robert Giegerich
    posted to pseudoknot review by eckart_bindewald on 2006-08-29 12:10:35 as **** along with 12 people and 4 groups marcius tardigrade andersbj arcticrasta mtagaya condon Hosna Eonwe cthachuk stajich physics reyez microRNA beta BioinfoCIPF SGU-CIPF
  • HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
    RNA, Vol. 11, No. 10. (October 2005), pp. 1494-1504.
    by J Ren, B Rastegari, A Condon, HH Hoos
    posted to pseudoknot rna secondary structure by eckart_bindewald on 2006-02-06 21:35:30 as ** along with 6 people and 3 groups marcius arcticrasta condon Hosna jarasch guxiyou beta BioinfoCIPF SGU-CIPF
  • Pseudo--half-knot formation with RNA.
    Science, Vol. 257, No. 5072. (14 August 1992), pp. 958-961.
    by DJ Ecker, TA Vickers, TW Bruice, SM Freier, RD Jenison, M Manoharan, M Zounes
    posted to pseudoknot rna by austin on 2007-09-03 01:06:43 as read
  • Induction of ribozyme activity by anti-ribozyme oligonucleotides.
    Nucleic Acids Symp Ser, No. 42. (1999), pp. 279-280.
    by Y Komatsu, S Yamashita, N Kazama, E Ohtsuka
    posted to activation hammerhead pseudoknot ribozyme by austin on 2007-09-03 15:07:16 as read
  • Pseudoknots: RNA structures with diverse functions.
    PLoS Biol, Vol. 3, No. 6. (June 2005)
    by DW Staple, SE Butcher
    posted to pseudoknot review rna by austin on 2008-02-29 19:54:36 as read along with 4 people and 3 groups marcius arcticrasta condon Hosna beta BioinfoCIPF SGU-CIPF
  • Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor
    Journal of Molecular Biology, Vol. 299, No. 5. (23 June 2000), pp. 1231-1243.
    by Yasuo Komatsu, Shigeko Yamashita, Nobuhiro Kazama, Kaoru Nobuoka, Eiko Ohtsuka
    posted to activation pseudoknot ribozyme by austin on 2007-09-03 00:42:23 as read
  • Regulation of ribozyme cleavage activity by oligonucleotides.
    Methods Mol Biol, Vol. 252 (2004), pp. 165-177.
    by Y Komatsu, E Ohtsuka
    posted to activation hairpin hammerhead pseudoknot ribozyme by austin on 2007-09-03 15:08:36 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
  • 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
  • Secondary Structure of Vertebrate Telomerase RNA
    Cell, Vol. 100, No. 5. (3 March 2000), pp. 503-514.
    by Jiunn-Liang Chen, Maria A Blasco, Carol W Greider
    posted to pseudoknot by aredash on 2007-04-04 18:07:03 as ** along with 1 person Hosna
  • The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein.
    Proc Natl Acad Sci U S A, Vol. 96, No. 12. (8 June 1999), pp. 6621-6625.
    by D Gilley, EH Blackburn
    posted to pseudoknot by aredash on 2007-04-04 17:42:51 as **
  • Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching.
    Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 753-758.
    by I Barrette, G Poisson, P Gendron, F Major
    posted to prion pseudoknot rnamot by arcticrasta on 2006-05-02 16:34:38 as **
  • Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2611-2617.
    by H Matsui, K Sato, Y Sakakibara
    posted to bioinformatics comparative prediction pseudoknot rna secondary structure by arcticrasta on 2006-06-05 19:21:10 as **
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