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Items: 1 to 20 of 108

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.

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.

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.

4.

Rtools: a web server for various secondary structural analyses on single RNA sequences.

Hamada M, Ono Y, Kiryu H, Sato K, Kato Y, Fukunaga T, Mori R, Asai K.

Nucleic Acids Res. 2016 Jul 8;44(W1):W302-7. doi: 10.1093/nar/gkw337. Epub 2016 Apr 29.

5.

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.

6.

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.

7.

Web-Beagle: a web server for the alignment of RNA secondary structures.

Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M.

Nucleic Acids Res. 2015 Jul 1;43(W1):W493-7. doi: 10.1093/nar/gkv489. Epub 2015 May 14.

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.

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.

10.

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.

11.

Vienna RNA secondary structure server.

Hofacker IL.

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

12.

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.

13.

MultiSETTER: web server for multiple RNA structure comparison.

Čech P, Hoksza D, Svozil D.

BMC Bioinformatics. 2015 Aug 12;16:253. doi: 10.1186/s12859-015-0696-8.

14.

An RNA secondary structure prediction method based on minimum and suboptimal free energy structures.

Fu H, Yang L, Zhang X.

J Theor Biol. 2015 Sep 7;380:473-9. doi: 10.1016/j.jtbi.2015.05.007. Epub 2015 Jun 20.

PMID:
26100179
15.

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.

16.

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

Knudsen B, Hein J.

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

17.

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.

18.

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.

19.

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.

20.

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

Miao Z, Westhof E.

Nucleic Acids Res. 2016 Jul 8;44(W1):W562-7. doi: 10.1093/nar/gkw251. Epub 2016 Apr 15.

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