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Results: 1 to 20 of 104

1.

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.

Puton T, Kozlowski LP, Rother KM, Bujnicki JM.

Nucleic Acids Res. 2013 Apr;41(7):4307-23. doi: 10.1093/nar/gkt101. Epub 2013 Feb 21. Erratum in: Nucleic Acids Res. 2014 Apr;42(8):5403-6.

PMID:
23435231
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.

Puton T, Kozlowski LP, Rother KM, Bujnicki JM.

Nucleic Acids Res. 2014 Apr;42(8):5403-6. doi: 10.1093/nar/gku208. Epub 2014 Mar 18. No abstract available.

PMID:
24682823
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

CENTROIDFOLD: a web server for RNA secondary structure prediction.

Sato K, Hamada M, Asai K, Mituyama T.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W277-80. doi: 10.1093/nar/gkp367. Epub 2009 May 12.

PMID:
19435882
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions.

Rath EM, Tessier D, Campbell AA, Lee HC, Werner T, Salam NK, Lee LK, Church WB.

BMC Bioinformatics. 2013 Mar 27;14:111. doi: 10.1186/1471-2105-14-111.

PMID:
23530628
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.

Hamada M, Yamada K, Sato K, Frith MC, Asai K.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W100-6. doi: 10.1093/nar/gkr290. Epub 2011 May 11.

PMID:
21565800
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
21685106
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.

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

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W29-34. doi: 10.1093/nar/gks412. Epub 2012 May 16.

PMID:
22600734
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.

Arunapuram P, Edvardsson I, Golden M, Anderson JW, Novák A, Sükösd Z, Hein J.

Bioinformatics. 2013 Mar 1;29(5):654-5. doi: 10.1093/bioinformatics/btt025. Epub 2013 Jan 17.

PMID:
23335014
[PubMed - indexed for MEDLINE]
Free Article
10.

Vienna RNA secondary structure server.

Hofacker IL.

Nucleic Acids Res. 2003 Jul 1;31(13):3429-31.

PMID:
12824340
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Predictions of RNA secondary structure by combining homologous sequence information.

Hamada M, Sato K, Kiryu H, Mituyama T, Asai K.

Bioinformatics. 2009 Jun 15;25(12):i330-8. doi: 10.1093/bioinformatics/btp228.

PMID:
19478007
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Automated 3D structure composition for large RNAs.

Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW.

Nucleic Acids Res. 2012 Aug;40(14):e112. doi: 10.1093/nar/gks339. Epub 2012 Apr 26.

PMID:
22539264
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
14.

Pfold: RNA secondary structure prediction using stochastic context-free grammars.

Knudsen B, Hein J.

Nucleic Acids Res. 2003 Jul 1;31(13):3423-8.

PMID:
12824339
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

FRASS: the web-server for RNA structural comparison.

Kirillova S, Tosatto SC, Carugo O.

BMC Bioinformatics. 2010 Jun 16;11:327. doi: 10.1186/1471-2105-11-327.

PMID:
20553602
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Gruber AR, Neuböck R, Hofacker IL, Washietl S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8. Epub 2007 Apr 22.

PMID:
17452347
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Predicting RNA structure using mutual information.

Freyhult E, Moulton V, Gardner P.

Appl Bioinformatics. 2005;4(1):53-9.

PMID:
16000013
[PubMed - indexed for MEDLINE]
18.

Prediction of RNA secondary structure using generalized centroid estimators.

Hamada M, Kiryu H, Sato K, Mituyama T, Asai K.

Bioinformatics. 2009 Feb 15;25(4):465-73. doi: 10.1093/bioinformatics/btn601. Epub 2008 Dec 18.

PMID:
19095700
[PubMed - indexed for MEDLINE]
Free Article
19.

ModeRNA server: an online tool for modeling RNA 3D structures.

Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM.

Bioinformatics. 2011 Sep 1;27(17):2441-2. doi: 10.1093/bioinformatics/btr400. Epub 2011 Jul 4.

PMID:
21727140
[PubMed - indexed for MEDLINE]
Free Article
20.

RNAstructure: Web servers for RNA secondary structure prediction and analysis.

Bellaousov S, Reuter JS, Seetin MG, Mathews DH.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W471-4. doi: 10.1093/nar/gkt290. Epub 2013 Apr 24.

PMID:
23620284
[PubMed - indexed for MEDLINE]
Free PMC Article

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