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Items: 1 to 20 of 214

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Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

Wu JC, Gardner DP, Ozer S, Gutell RR, Ren P.

J Mol Biol. 2009 Aug 28;391(4):769-83. doi: 10.1016/j.jmb.2009.06.036. Epub 2009 Jun 18.

4.

RNA secondary structure prediction based on free energy and phylogenetic analysis.

Juan V, Wilson C.

J Mol Biol. 1999 Jun 18;289(4):935-47.

PMID:
10369773
5.

Accurate SHAPE-directed RNA structure determination.

Deigan KE, Li TW, Mathews DH, Weeks KM.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102. doi: 10.1073/pnas.0806929106. Epub 2008 Dec 24.

6.

Secondary structure and domain architecture of the 23S and 5S rRNAs.

Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD.

Nucleic Acids Res. 2013 Aug;41(15):7522-35. doi: 10.1093/nar/gkt513. Epub 2013 Jun 14.

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SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.

Tsang HH, Wiese KC.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):727-40. doi: 10.1109/TCBB.2008.97.

PMID:
21030739
10.

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
11.

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.

Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR.

BMC Bioinformatics. 2002;3:2. Epub 2002 Jan 17. Erratum in: BMC Bioinformatics. 2002 Jul;3(1):15.

12.

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

Gutell RR, Larsen N, Woese CR.

Microbiol Rev. 1994 Mar;58(1):10-26. Review.

13.

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.

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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.

17.

Structural constraints identified with covariation analysis in ribosomal RNA.

Shang L, Xu W, Ozer S, Gutell RR.

PLoS One. 2012;7(6):e39383. doi: 10.1371/journal.pone.0039383. Epub 2012 Jun 19.

19.

Sequence and structural conservation in RNA ribose zippers.

Tamura M, Holbrook SR.

J Mol Biol. 2002 Jul 12;320(3):455-74.

PMID:
12096903
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