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Items: 1 to 20 of 110

1.

DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle.

Wang L, Liu Y, Zhong X, Liu H, Lu C, Li C, Zhang H.

Front Genet. 2019 Mar 4;10:143. doi: 10.3389/fgene.2019.00143. eCollection 2019.

2.

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
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.

Prediction of RNA secondary structure with pseudoknots using integer programming.

Poolsap U, Kato Y, Akutsu T.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S38. doi: 10.1186/1471-2105-10-S1-S38.

5.

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
6.

[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
7.

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.

8.

Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.

Legendre A, Angel E, Tahi F.

BMC Bioinformatics. 2018 Jan 15;19(1):13. doi: 10.1186/s12859-018-2007-7.

9.

TOPAS: network-based structural alignment of RNA sequences.

Chen CC, Jeong H, Qian X, Yoon BJ.

Bioinformatics. 2019 Jan 10. doi: 10.1093/bioinformatics/btz001. [Epub ahead of print]

PMID:
30629122
10.

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

Danaee P, Rouches M, Wiley M, Deng D, Huang L, Hendrix D.

Nucleic Acids Res. 2018 Jun 20;46(11):5381-5394. doi: 10.1093/nar/gky285.

11.

RNA pseudoknot prediction in energy-based models.

Lyngsø RB, Pedersen CN.

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

PMID:
11108471
12.
13.

[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
14.

Predicting pseudoknotted structures across two RNA sequences.

Sperschneider J, Datta A, Wise MJ.

Bioinformatics. 2012 Dec 1;28(23):3058-65. doi: 10.1093/bioinformatics/bts575. Epub 2012 Oct 8.

15.

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

Yehdego DT, Zhang B, Kodimala VK, Johnson KL, Taufer M, Leung MY.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2013 May;2013:520-529.

16.

K-partite RNA secondary structures.

Jiang M, Tejada PJ, Lasisi RO, Cheng S, Fechser DS.

J Comput Biol. 2010 Jul;17(7):915-25. doi: 10.1089/cmb.2009.0119.

PMID:
20632871
17.

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.

Jabbari H, Condon A.

BMC Bioinformatics. 2014 May 18;15:147. doi: 10.1186/1471-2105-15-147.

18.

A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures.

Tsang HH, Wiese KC.

Int J Bioinform Res Appl. 2015;11(5):375-96.

PMID:
26558299
19.

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.

20.

RNA folding on the 3D triangular lattice.

Gillespie J, Mayne M, Jiang M.

BMC Bioinformatics. 2009 Nov 5;10:369. doi: 10.1186/1471-2105-10-369.

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