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Results: 1 to 20 of 132

1.

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

Rivas E, Lang R, Eddy SR.

RNA. 2012 Feb;18(2):193-212. doi: 10.1261/rna.030049.111. Epub 2011 Dec 22.

PMID:
22194308
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

CONTRAfold: RNA secondary structure prediction without physics-based models.

Do CB, Woods DA, Batzoglou S.

Bioinformatics. 2006 Jul 15;22(14):e90-8.

PMID:
16873527
[PubMed - indexed for MEDLINE]
Free Article
3.

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
[PubMed - indexed for MEDLINE]
4.

Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures.

Scheid A, Nebel ME.

BMC Bioinformatics. 2012 Jul 9;13:159. doi: 10.1186/1471-2105-13-159.

PMID:
22776037
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
6.

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
7.

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

Dowell RD, Eddy SR.

BMC Bioinformatics. 2004 Jun 4;5:71.

PMID:
15180907
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction.

Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR.

BMC Bioinformatics. 2004 Aug 5;5:105.

PMID:
15296519
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Accelerated probabilistic inference of RNA structure evolution.

Holmes I.

BMC Bioinformatics. 2005 Mar 24;6:73.

PMID:
15790387
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Analysis of the free energy in a stochastic RNA secondary structure model.

Nebel ME, Scheid A.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Nov-Dec;8(6):1468-82. doi: 10.1109/TCBB.2010.126.

PMID:
21116040
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
19933322
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.

Turner DH, Mathews DH.

Nucleic Acids Res. 2010 Jan;38(Database issue):D280-2. doi: 10.1093/nar/gkp892. Epub 2009 Oct 30.

PMID:
19880381
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Statistical and Bayesian approaches to RNA secondary structure prediction.

Ding Y.

RNA. 2006 Mar;12(3):323-31. Review.

PMID:
16495231
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22296803
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

RnaPredict--an evolutionary algorithm for RNA secondary structure prediction.

Wiese KC, Deschenes AA, Hendriks AG.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):25-41. doi: 10.1109/tcbb.2007.1054.

PMID:
18245873
[PubMed - indexed for MEDLINE]
16.

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.

Janssen S, Schudoma C, Steger G, Giegerich R.

BMC Bioinformatics. 2011 Nov 3;12:429. doi: 10.1186/1471-2105-12-429.

PMID:
22051375
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Characterising RNA secondary structure space using information entropy.

Sükösd Z, Knudsen B, Anderson JW, Novák A, Kjems J, Pedersen CN.

BMC Bioinformatics. 2013;14 Suppl 2:S22. doi: 10.1186/1471-2105-14-S2-S22. Epub 2013 Jan 21.

PMID:
23368905
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Evolutionary models for insertions and deletions in a probabilistic modeling framework.

Rivas E.

BMC Bioinformatics. 2005 Mar 21;6:63.

PMID:
15780137
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.

Lu ZJ, Turner DH, Mathews DH.

Nucleic Acids Res. 2006;34(17):4912-24. Epub 2006 Sep 18.

PMID:
16982646
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

RNAalifold: improved consensus structure prediction for RNA alignments.

Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF.

BMC Bioinformatics. 2008 Nov 11;9:474. doi: 10.1186/1471-2105-9-474.

PMID:
19014431
[PubMed - indexed for MEDLINE]
Free PMC Article

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