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Results: 1 to 20 of 100

1.

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Proctor JR, Meyer IM.

Nucleic Acids Res. 2013 May;41(9):e102. doi: 10.1093/nar/gkt174. Epub 2013 Mar 19.

PMID:
23511969
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

On the importance of cotranscriptional RNA structure formation.

Lai D, Proctor JR, Meyer IM.

RNA. 2013 Nov;19(11):1461-73. doi: 10.1261/rna.037390.112. Review.

PMID:
24131802
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.

Harmanci AO, Sharma G, Mathews DH.

BMC Bioinformatics. 2011 Apr 20;12:108. doi: 10.1186/1471-2105-12-108.

PMID:
21507242
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Cotranscriptional folding kinetics of ribonucleic acid secondary structures.

Zhao P, Zhang W, Chen SJ.

J Chem Phys. 2011 Dec 28;135(24):245101. doi: 10.1063/1.3671644.

PMID:
22225186
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Co-transcriptional folding is encoded within RNA genes.

Meyer IM, Miklós I.

BMC Mol Biol. 2004 Aug 6;5:10.

PMID:
15298702
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

Al-Khatib RM, Rashid NA, Abdullah R.

J Biomol Struct Dyn. 2011 Aug;29(1):1-26.

PMID:
21696223
[PubMed - indexed for MEDLINE]
7.

The computer simulation of RNA folding involving pseudoknot formation.

Gultyaev AP.

Nucleic Acids Res. 1991 May 11;19(9):2489-94.

PMID:
1710358
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.

Anderson JW, Haas PA, Mathieson LA, Volynkin V, Lyngsø R, Tataru P, Hein J.

Bioinformatics. 2013 Mar 15;29(6):704-10. doi: 10.1093/bioinformatics/btt050. Epub 2013 Feb 8.

PMID:
23396120
[PubMed - indexed for MEDLINE]
Free Article
9.

The computer simulation of RNA folding pathways using a genetic algorithm.

Gultyaev AP, van Batenburg FH, Pleij CW.

J Mol Biol. 1995 Jun 30;250(1):37-51.

PMID:
7541471
[PubMed - indexed for MEDLINE]
10.

Prediction of RNA secondary structure based on helical regions distribution.

WuJu L, JiaJin W.

Bioinformatics. 1998;14(8):700-6.

PMID:
9790689
[PubMed - indexed for MEDLINE]
Free Article
11.

Consensus folding of unaligned RNA sequences revisited.

Bafna V, Tang H, Zhang S.

J Comput Biol. 2006 Mar;13(2):283-95.

PMID:
16597240
[PubMed - indexed for MEDLINE]
12.

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.

Rivas E.

RNA Biol. 2013 Jul;10(7):1185-96. doi: 10.4161/rna.24971. Epub 2013 May 10.

PMID:
23695796
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Dynamic extended folding: modeling the RNA secondary structures during co-transcriptional folding.

Cao H, Xie HZ, Zhang W, Wang K, Li W, Liu CQ.

J Theor Biol. 2009 Nov 7;261(1):93-9. doi: 10.1016/j.jtbi.2009.07.027. Epub 2009 Jul 28.

PMID:
19643109
[PubMed - indexed for MEDLINE]
14.

A kinetic model of RNA folding.

Mironov AA, Lebedev VF.

Biosystems. 1993;30(1-3):49-56.

PMID:
7690611
[PubMed - indexed for MEDLINE]
15.

A graphical tool for parametric simulation of the RNA structure formation.

Han K.

Mol Cells. 2000 Jun 30;10(3):348-55.

PMID:
10901175
[PubMed - indexed for MEDLINE]
Free Article
16.

RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.

Avihoo A, Churkin A, Barash D.

BMC Bioinformatics. 2011 Aug 3;12:319. doi: 10.1186/1471-2105-12-319.

PMID:
21813013
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

Wiebe NJ, Meyer IM.

PLoS Comput Biol. 2010 Jun 24;6(6):e1000823. doi: 10.1371/journal.pcbi.1000823.

PMID:
20589081
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Improving the accuracy of predicting secondary structure for aligned RNA sequences.

Hamada M, Sato K, Asai K.

Nucleic Acids Res. 2011 Jan;39(2):393-402. doi: 10.1093/nar/gkq792. Epub 2010 Sep 15.

PMID:
20843778
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.

Tsang HH, Wiese KC.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):727-40. doi: 10.1109/TCBB.2008.97.

PMID:
21030739
[PubMed - indexed for MEDLINE]
20.

Deleterious mutation prediction in the secondary structure of RNAs.

Barash D.

Nucleic Acids Res. 2003 Nov 15;31(22):6578-84.

PMID:
14602917
[PubMed - indexed for MEDLINE]
Free PMC Article

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