RNA secondary structure prediction.

David H Mathews, Douglas H Turner, Michael Zuker

Author Information

David H Mathews: University of Rochester, Rochester, New York, USA.

PMID: 18428968 DOI: 10.1002/0471142700.nc1102s28

Details for predicting secondary structure of RNA sequences using free energy minimization are given. Protocols present the use of the RNAstructure computer program (for PCs) and the mfold server (for Unix platforms). The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented.

Nucleic Acids Res. 1987 Nov 25;15(22):9109-28 [PMID: 2446263]
Nucleic Acids Res. 2003 Sep 1;31(17):4989-94 [PMID: 12930948]
Nucleic Acids Res. 2008 Feb;36(2):640-7 [PMID: 18073195]
Nat Biotechnol. 2004 Nov;22(11):1457-8 [PMID: 15529172]
J Mol Biol. 1999 May 21;288(5):911-40 [PMID: 10329189]
Biochemistry. 1998 Oct 20;37(42):14719-35 [PMID: 9778347]
Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102 [PMID: 19109441]
J Mol Biol. 1999 Feb 5;285(5):2053-68 [PMID: 9925784]
Nucleic Acids Res. 2006;34(17):4912-24 [PMID: 16982646]
Nucleic Acids Res. 2005 Feb 18;33(3):e30 [PMID: 15722476]
Methods Enzymol. 1989;180:192-212 [PMID: 2482414]
Nucleic Acids Res. 1995 Jul 25;23(14):2791-8 [PMID: 7544463]
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92 [PMID: 15123812]
Nucleic Acids Res. 1999 Jan 1;27(1):314 [PMID: 9847214]
Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218-22 [PMID: 7524072]
J Biol Chem. 2003 May 2;278(18):15991-7 [PMID: 12604614]
RNA. 1999 Nov;5(11):1458-69 [PMID: 10580474]
Nucleic Acids Res. 2003 Jul 1;31(13):3429-31 [PMID: 12824340]
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D139-40 [PMID: 15608164]
RNA. 2010 Oct;16(10):1870-80 [PMID: 20699301]
RNA. 2009 Oct;15(10):1805-13 [PMID: 19703939]
RNA. 2004 Aug;10(8):1178-90 [PMID: 15272118]
Nucleic Acids Res. 2003 Aug 1;31(15):4417-24 [PMID: 12888501]
Biochem Pharmacol. 2003 Sep 1;66(5):819-30 [PMID: 12948863]
RNA. 1996 Dec;2(12):1306-10 [PMID: 8972778]
Science. 1989 Apr 7;244(4900):48-52 [PMID: 2468181]
BMC Bioinformatics. 2004 Jun 04;5:71 [PMID: 15180907]
J Comput Chem. 2003 Oct;24(13):1664-77 [PMID: 12926009]
RNA. 1998 Jun;4(6):669-79 [PMID: 9622126]

R01 GM022939/NIGMS NIH HHS
R01 GM076485/NIGMS NIH HHS

Nucleic Acid Conformation

Probability

RNA

Journal Article

RNA Secondary Structure Prediction.Prediction of RNA secondary structure.RNA-SSPT: RNA Secondary Structure Prediction Tools.SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach.In Silico Prediction of RNA Secondary Structure.Genome-Wide RNA Secondary Structure Prediction.Computational prediction of RNA secondary structure.RNA secondary structure prediction using soft computing.SHAPE-directed RNA secondary structure prediction.Secondary structure prediction for aligned RNA sequences.

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