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Items: 1 to 20 of 158

1.

Computational approaches for RNA energy parameter estimation.

Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP.

RNA. 2010 Dec;16(12):2304-18. doi: 10.1261/rna.1950510. Epub 2010 Oct 12.

2.

Improved free energy parameters for RNA pseudoknotted secondary structure prediction.

Andronescu MS, Pop C, Condon AE.

RNA. 2010 Jan;16(1):26-42. doi: 10.1261/rna.1689910. Epub 2009 Nov 20.

3.

Efficient parameter estimation for RNA secondary structure prediction.

Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP.

Bioinformatics. 2007 Jul 1;23(13):i19-28.

PMID:
17646296
4.

Analysis of energy-based algorithms for RNA secondary structure prediction.

Hajiaghayi M, Condon A, Hoos HH.

BMC Bioinformatics. 2012 Feb 1;13:22. doi: 10.1186/1471-2105-13-22.

5.

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

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

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

6.

Ensemble-based prediction of RNA secondary structures.

Aghaeepour N, Hoos HH.

BMC Bioinformatics. 2013 Apr 24;14:139. doi: 10.1186/1471-2105-14-139.

7.

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.

8.

Secondary structure prediction of interacting RNA molecules.

Andronescu M, Zhang ZC, Condon A.

J Mol Biol. 2005 Feb 4;345(5):987-1001. Epub 2004 Dec 16.

PMID:
15644199
9.

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
10.

Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.

Bleckley S, Stone JW, Schroeder SJ.

PLoS One. 2012;7(12):e52414. doi: 10.1371/journal.pone.0052414. Epub 2012 Dec 27.

11.

[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
12.

Evaluation of a sophisticated SCFG design for RNA secondary structure prediction.

Nebel ME, Scheid A.

Theory Biosci. 2011 Dec;130(4):313-36. doi: 10.1007/s12064-011-0139-7. Epub 2011 Dec 2.

PMID:
22135038
13.

The RNA Newton polytope and learnability of energy parameters.

Forouzmand E, Chitsaz H.

Bioinformatics. 2013 Jul 1;29(13):i300-7. doi: 10.1093/bioinformatics/btt226.

14.

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.

15.

A statistical sampling algorithm for RNA secondary structure prediction.

Ding Y, Lawrence CE.

Nucleic Acids Res. 2003 Dec 15;31(24):7280-301.

16.

Free energy minimization to predict RNA secondary structures and computational RNA design.

Churkin A, Weinbrand L, Barash D.

Methods Mol Biol. 2015;1269:3-16. doi: 10.1007/978-1-4939-2291-8_1.

PMID:
25577369
17.

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.

Mathews DH, Turner DH.

J Mol Biol. 2002 Mar 22;317(2):191-203.

PMID:
11902836
18.

Prediction of RNA secondary structure based on helical regions distribution.

WuJu L, JiaJin W.

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

PMID:
9790689
19.

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.

Harmanci AO, Sharma G, Mathews DH.

BMC Bioinformatics. 2007 Apr 19;8:130.

20.

RNA structure prediction from evolutionary patterns of nucleotide composition.

Smit S, Knight R, Heringa J.

Nucleic Acids Res. 2009 Apr;37(5):1378-86. doi: 10.1093/nar/gkn987. Epub 2009 Jan 7.

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