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Items: 1 to 20 of 340

1.

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

Bellaousov S, Mathews DH.

RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310. Epub 2010 Aug 10.

2.

Prediction of consensus RNA secondary structures including pseudoknots.

Witwer C, Hofacker IL, Stadler PF.

IEEE/ACM Trans Comput Biol Bioinform. 2004 Apr-Jun;1(2):66-77.

PMID:
17048382
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.

4.

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

Ruan J, Stormo GD, Zhang W.

Bioinformatics. 2004 Jan 1;20(1):58-66.

PMID:
14693809
5.

RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment.

Xu X, Ji Y, Stormo GD.

Bioinformatics. 2007 Aug 1;23(15):1883-91. Epub 2007 May 30.

PMID:
17537756
6.

Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins.

Sperschneider J, Datta A, Wise MJ.

RNA. 2011 Jan;17(1):27-38. doi: 10.1261/rna.2394511. Epub 2010 Nov 22.

7.

RNAstructure: software for RNA secondary structure prediction and analysis.

Reuter JS, Mathews DH.

BMC Bioinformatics. 2010 Mar 15;11:129. doi: 10.1186/1471-2105-11-129.

8.

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.

Sato K, Kato Y, Hamada M, Akutsu T, Asai K.

Bioinformatics. 2011 Jul 1;27(13):i85-93. doi: 10.1093/bioinformatics/btr215.

9.

Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs.

Ieong S, Kao MY, Lam TW, Sung WK, Yiu SM.

J Comput Biol. 2003;10(6):981-95.

PMID:
14980021
10.

KnotSeeker: heuristic pseudoknot detection in long RNA sequences.

Sperschneider J, Datta A.

RNA. 2008 Apr;14(4):630-40. doi: 10.1261/rna.968808. Epub 2008 Feb 26.

11.

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

Ren J, Rastegari B, Condon A, Hoos HH.

RNA. 2005 Oct;11(10):1494-504.

12.

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

Matsui H, Sato K, Sakakibara Y.

Proc IEEE Comput Syst Bioinform Conf. 2004:290-9.

PMID:
16448022
13.

RNA pseudoknot prediction in energy-based models.

Lyngsø RB, Pedersen CN.

J Comput Biol. 2000;7(3-4):409-27.

PMID:
11108471
14.

Novel and efficient RNA secondary structure prediction using hierarchical folding.

Jabbari H, Condon A, Zhao S.

J Comput Biol. 2008 Mar;15(2):139-63. doi: 10.1089/cmb.2007.0198.

PMID:
18312147
15.

[Predicting RNA secondary structures including pseudoknots by covariance with stacking and minimum free energy].

Yang J, Luo Z, Fang X, Wang J, Tang K.

Sheng Wu Gong Cheng Xue Bao. 2008 Apr;24(4):659-64. Chinese.

PMID:
18616179
16.

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.

Ji Y, Xu X, Stormo GD.

Bioinformatics. 2004 Jul 10;20(10):1591-602. Epub 2004 Feb 12.

PMID:
14962926
17.

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.

Xu Z, Mathews DH.

Bioinformatics. 2011 Mar 1;27(5):626-32. doi: 10.1093/bioinformatics/btq726. Epub 2010 Dec 30.

18.

Predicting RNA-RNA Interactions Using RNAstructure.

DiChiacchio L, Mathews DH.

Methods Mol Biol. 2016;1490:51-62. doi: 10.1007/978-1-4939-6433-8_4.

PMID:
27665592
19.

[An iterative method for prediction of RNA secondary structures including pseudoknots based on minimum of free energy and covariance].

Wang ZX, Luo ZG, Guan NY, Yan FM, Jin X, Zhang W.

Yi Chuan. 2007 Jul;29(7):889-97. Chinese.

PMID:
17646157
20.

The computer simulation of RNA folding involving pseudoknot formation.

Gultyaev AP.

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

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