Tag pseudoknot [60 articles] Export

Recent papers classified by the tag pseudoknot.

	Predicting structures and stabilities for H-type pseudoknots with interhelix loops. [My Copy] RNA (New York, N.Y.), Vol. 15, No. 4. (April 2009), pp. 696-706. by Song Cao, Shi-Jie J. Chen posted to pseudoknots pseudoknot by Hosna on 2009-11-30 23:19:26 as along with 1 person physics
	Structural and functional aspects of RNA pseudoknots. [My Copy] Biochemistry, Vol. 31, No. 47. (1 December 1992), pp. 11665-11676. by E. Dam, K. Pleij, D. Draper posted to rna pseudoknot paper ncrna biochemistry by thomaskf on 2009-11-24 03:15:58 as
	Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding [My Copy] PLoS ONE, Vol. 2, No. 9. (2007), e905. by Wayne K. Dawson, Kazuya Fujiwara, Gota Kawai posted to pseudoknot by heliopais on 2009-09-11 07:45:33 as along with 1 person nikkiwithers
	FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space [My Copy] Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 1994-2001. by Xiang Chen, Si-Min He, Dongbo Bu, et al.Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao posted to pseudoknot by heliopais on 2009-09-11 07:44:44 as
	The language of RNA: a formal grammar that includes pseudoknots [My Copy] Bioinformatics, Vol. 16, No. 4. (1 April 2000), pp. 334-340. by Elena Rivas, Sean R. Eddy posted to pseudoknot by heliopais on 2009-09-11 07:44:17 as along with 5 people and 2 groups gemammr evaf condon Hosna cthachuk GEB beta
	An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots [My Copy] Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 58-66. by Jianhua Ruan, Gary D. Stormo, Weixiong Zhang posted to pseudoknot by heliopais on 2009-09-11 07:43:46 as along with 4 people and 1 group evaf arcticrasta condon Hosna beta
	Fast and accurate search for non-coding RNA pseudoknot structures in genomes [My Copy] Bioinformatics, Vol. 24, No. 20. (15 October 2008), pp. 2281-2287. by Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L. Malmberg, Liming Cai posted to pseudoknot by heliopais on 2009-09-11 07:43:10 as along with 6 people zanexu mhamada samgj djkt Ema papamicd
	Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (23 July 2009) by Gang Chen, Kung-Yao Y. Chang, Ming-Yuan Y. Chou, Carlos Bustamante, Ignacio Tinoco posted to frameshifting optical_tweezers pseudoknot ribosome rna unfolding by alexknight on 2009-08-03 13:19:00 as along with 1 person physics
	The influence of single base triplet changes on the stability of a pur.pur.pyr triple helix determined by affinity cleaving. [My Copy] Nucleic acids research, Vol. 20, No. 11. (11 June 1992), pp. 2773-2776. by P. A. Beal, P. B. Dervan posted to cleavage dervan feedta hydroxyl pseudoknot radical triplet by mihalus on 2009-07-03 23:03:36 as
	PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1435-1437. by Yanga Byun, Kyungsook Han posted to pseudoknot rna software by AlexBateman to the group Journal picks on 2009-05-20 11:55:40 as along with 1 person reyez
	Statistics of canonical RNA pseudoknot structures [My Copy] Journal of Theoretical Biology, Vol. 253, No. 3. (07 August 2008), pp. 570-578. by Fenix W. Huang, Christian M. Reidys posted to pseudoknot rna statistics by gzm55 to the group CBPC@CFC on 2009-05-20 05:53:44 as
	Combinatorics of RNA Structures with Pseudoknots [My Copy] Bulletin of Mathematical Biology, Vol. 70, No. 1. (1 January 2008), pp. 45-67. by Emma Y. Jin, Jing Qin, Christian M. Reidys posted to combinatorics pseudoknot rna by gzm55 to the group CBPC@CFC on 2009-05-20 05:53:07 as
	Folding 3-noncrossing RNA pseudoknot structures [My Copy] (29 Sep 2008) by Fenix W. Huang, Wade W. Peng, Christian M. Reidys posted to algorithm dynamic-programming prediction pseudoknot rna by gzm55 to the group CBPC@CFC on 2009-05-20 05:52:31 as
	Canonical RNA pseudoknot structures [My Copy] Journal of Computational Biology, Vol. 15, No. 10. (December 2008), pp. 1257-1273. by Gang Ma, Christian M. Reidys posted to combinatorics pseudoknot rna by gzm55 to the group CBPC@CFC on 2009-05-20 05:51:32 as
	A combinatorial framework for RNA tertiary interaction [My Copy] (8 Dec 2007) by Jing Qin, Christian M. Reidys posted to combinatorics pseudoknot rna by gzm55 to the group CBPC@CFC on 2009-05-20 05:48:56 as
	RNA pseudoknots [My Copy] Current Opinion in Structural Biology, Vol. 2, No. 3. (June 1992), pp. 327-333. by L. Jaeger, Eric Westhof posted to pseudoknot rna by gzm55 on 2009-05-20 05:32:15 as
	RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties [My Copy] Bulletin of Mathematical Biology, Vol. 61, No. 3. (1 May 1999), pp. 437-467. by Christian Haslinger, Peter F. Stadler posted to combinatorics graph pseudoknot rna statistics by gzm55 on 2009-05-19 09:17:33 as along with 1 person jmallos
	HotKnots: heuristic prediction of RNA secondary structures including pseudoknots [My Copy] RNA, Vol. 11, No. 10. (October 2005), pp. 1494-1504. by J. Ren, B. Rastegari, A. Condon, H. H. Hoos posted to heuristic-algorithm prediction pseudoknot rna by gzm55 on 2009-05-19 08:56:24 as along with 9 people and 3 groups haarcuba rb_india marcius eckart_bindewald arcticrasta condon Hosna jarasch guxiyou beta BioinfoCIPF SGU-CIPF
	A dynamic programming algorithm for RNA structure prediction including pseudoknots [My Copy] Journal of Molecular Biology, Vol. 285, No. 5. (05 February 1999), pp. 2053-2068. by Elena Rivas, Sean R. Eddy posted to algorithm dynamic-programming prediction pseudoknot rna by gzm55 on 2009-05-19 07:24:01 as along with 13 people and 1 group rb_india NicholasErho mjoach evaf balajis eckart_bindewald arcticrasta dquest condon Hosna jarasch physics guxiyou beta
	An RNA folding method capable of identifying pseudoknots and base triples [My Copy] Bioinformatics, Vol. 14, No. 8. (1 September 1998), pp. 691-699. by J. E. Tabaska, R. B. Cary, H. N. Gabow, G. D. Stormo posted to prediction pseudoknot rna rna-secondary-structure by gzm55 on 2009-05-19 06:47:04 as along with 2 people arcticrasta guxiyou
	RNA pseudoknot prediction in energy-based models [My Copy] Journal of Computational Biology, Vol. 7, No. 3-4. (7 August 2000), pp. 409-427. by R. B. Lyngsø, C. N. S. Pedersen posted to inverse-fold pseudoknot rna thermodynamics by gzm55 on 2009-05-18 04:25:44 as along with 5 people and 1 group evaf arcticrasta condon Hosna guxiyou beta
	Predicting RNA pseudoknot folding thermodynamics [My Copy] Nucleic Acids Research, Vol. 34, No. 9. (18 May 2006), pp. 2634-2652. by Song Cao, Shi J. Chen posted to biophysics prediction pseudoknot rna thermodynamics by gzm55 on 2009-05-18 01:29:54 as along with 5 people and 1 group condon Hosna apop physics Kiarostami beta
	Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots [My Copy] Discrete Applied Mathematics, Vol. 104, No. 1-3. (15 August 2000), pp. 45-62. by Tatsuya Akutsu posted to approximation-algorithms computational-biology dynamic-programming pseudoknot rna-secondary-structure by gzm55 on 2009-05-15 11:57:02 as along with 2 people and 1 group condon Hosna beta
	Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. [My Copy] J Mol Biol, Vol. 298, No. 2. (28 April 2000), pp. 167-185. by D. P. Giedroc, C. A. Theimer, P. L. Nixon posted to pseudoknot rna by nikkiwithers on 2009-05-06 10:14:06 as along with 3 people and 1 group condon Hosna physics beta
	Frameshifting RNA pseudoknots: structure and mechanism. [My Copy] Virus research, Vol. 139, No. 2. (February 2009), pp. 193-208. by D. P. Giedroc, P. V. Cornish posted to frameshift pseudoknot rna by nikkiwithers on 2009-04-29 21:03:31 as
	Apical loop-internal loop RNA pseudoknots: a new type of stimulator of -1 translational frameshifting in bacteria. [My Copy] The Journal of biological chemistry, Vol. 283, No. 29. (18 July 2008), pp. 20421-20432. by M. H. Mazauric, P. Licznar, M. F. Prère, I. Canal, O. Fayet posted to frameshift pseudoknot by nikkiwithers on 2009-04-13 09:19:59 as
	Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. [My Copy] RNA (New York, N.Y.), 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 3 people balewis carmaus Hosna
	PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals [My Copy] 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
	Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. [My Copy] 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 kinefold kinetics modeling pseudoknot rna by austin on 2008-04-15 18:02:44 as along with 6 people and 3 groups evaf marcius arcticrasta condon Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
	Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme [My Copy] 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 along with 4 people ellarond eckart_bindewald Hosna Kiarostami
	A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal [My Copy] 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
	Identification of functional, endogenous programmed 1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae [My Copy] Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. 165-174. by Jacobs, L. Jonathan, Belew, et al.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
	The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. [My Copy] RNA, Vol. 9, No. 2. (February 2003), pp. 168-174. by E. P. Plant, K. L. Jacobs, J. W. Harger, et al.A. Meskauskas, J. L. Jacobs, J. L. Baxter, A. N. Petrov, J. D. Dinman posted to genetics codon frameshift molecular mrna pseudoknot ribosome rna trna by jonathanjacobs on 2008-03-28 04:21:39 as along with 2 people physics KristiMuldoonJacobs
	Novel and efficient RNA secondary structure prediction using hierarchical folding. [My Copy] 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
	KnotSeeker: Heuristic pseudoknot detection in long RNA sequences [My Copy] 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 [My Copy] 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
	Pseudoknots: RNA structures with diverse functions. [My Copy] PLoS Biol, Vol. 3, No. 6. (June 2005) by D. W. Staple, S. E. Butcher posted to pseudoknot review rna by austin on 2008-02-29 19:54:36 as along with 5 people and 3 groups rb_india marcius arcticrasta condon Hosna beta BioinfoCIPF SGU-CIPF
	Regulation of ribozyme cleavage activity by oligonucleotides. [My Copy] 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
	Induction of ribozyme activity by anti-ribozyme oligonucleotides. [My Copy] 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
	Pseudo--half-knot formation with RNA. [My Copy] Science, Vol. 257, No. 5072. (14 August 1992), pp. 958-961. by D. J. Ecker, T. A. Vickers, T. W. Bruice, et al.S. M. Freier, R. D. Jenison, M. Manoharan, M. Zounes posted to pseudoknot rna by austin on 2007-09-03 01:06:43 as
	Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor [My Copy] 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
	A new principle of RNA folding based on pseudoknotting. [My Copy] Nucleic Acids Res, Vol. 13, No. 5. (11 March 1985), pp. 1717-1731. by C. W. Pleij, K. Rietveld, L. Bosch posted to folding pseudoknot rna by austin on 2007-08-28 20:27:56 as
	Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_2. (1 July 2005), pp. W605-610. by A. Xayaphoummine, T. Bucher, H. Isambert posted to kinefold kinetics prediction pseudoknot rna structure website by austin on 2007-08-27 14:38:30 as along with 4 people haarcuba oteri ellarond Kiarostami
	ILM: a web server for predicting RNA secondary structures with pseudoknots [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_2. (1 July 2004), pp. W146-149. by Jianhua Ruan, Gary D. Stormo, Weixiong Zhang posted to folding prediction pseudoknot rna website by austin on 2007-08-27 14:35:42 as along with 2 people haarcuba balajis
	Non-AUG-Initiated Internal Translation of the L* Protein of Theiler's Virus and Importance of This Protein for Viral Persistence [My Copy] 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 [My Copy] 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
	Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. [My Copy] J Mol Biol, Vol. 367, No. 3. (30 March 2007), pp. 909-924. by S. Cao, S. J. Chen posted to kinetics pseudoknot rna telomerase by physics on 2007-05-05 22:48:13 as
	Torsional restraint: a new twist on frameshifting pseudoknots [My Copy] 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
	A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting [My Copy] Nature, Vol. 441, No. 7090., pp. 244-247. by Olivier Namy, Stephen J. Moran, David I. Stuart, Robert J. C. Gilbert, Ian Brierley posted to force frameshifting pseudoknot by physics on 2007-05-05 22:34:13 as
	Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting [My Copy] 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

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rna	68
prediction	16
structure	9
combinatorics	7
frameshift	7
frameshifting	7
ncrna	7
secondary_structure_prediction	7
dynamic-programming	4
folding	4
force	4
kinefold	4
kinetics	4
mrna	4
paper	4
ribosome	4
secondary	4
secondary_structure	4
statistics	4
thermodynamics	4
activation	3
algorithm	3
biophysics	3
computational	3
database	3
jcb	3
review	3
ribozyme	3
structure_prediction	3
bioinformatics	2
bmc_bioinfo	2
cerevisiae	2
codon	2
energy-model	2
folding-pathways	2
genetics	2
genomics	2
hairpin	2
hammerhead	2
jmb	2
nature	2
prion	2
protein	2
rna-secondary-structure	2
saccharomyces	2
software	2
translation	2
virus	2
website	2
yeast	2
alignment	1
alzheimer	1
approximation-algorithms	1
biochemistry	1
biology	1
cleavage	1
comparative	1
comparative_apparoach	1
computational-biology	1
coronavirus	1
decay	1
dervan	1
feedta	1
genbank	1
genome	1
graph	1
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hydroxyl	1
inverse-fold	1
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phylogenetic	1
plos	1
pnas	1
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pseudoknots	1
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rnamot	1
structural_alignment	1
telomerase	1
tertiary	1
transcription	1
triplet	1
trna	1
unfolding	1
unread	1
viral	1

Tag pseudoknot [60 articles] Export

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