Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 106

1.

On the importance of cotranscriptional RNA structure formation.

Lai D, Proctor JR, Meyer IM.

RNA. 2013 Nov;19(11):1461-73. doi: 10.1261/rna.037390.112. Review.

2.

Cotranscriptional folding kinetics of ribonucleic acid secondary structures.

Zhao P, Zhang W, Chen SJ.

J Chem Phys. 2011 Dec 28;135(24):245101. doi: 10.1063/1.3671644.

3.

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Proctor JR, Meyer IM.

Nucleic Acids Res. 2013 May;41(9):e102. doi: 10.1093/nar/gkt174. Epub 2013 Mar 19.

4.

Cotranscriptional folding of a riboswitch at nucleotide resolution.

Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB.

Nat Struct Mol Biol. 2016 Dec;23(12):1124-1131. doi: 10.1038/nsmb.3316. Epub 2016 Oct 31.

PMID:
27798597
5.

Predicting pseudoknotted structures across two RNA sequences.

Sperschneider J, Datta A, Wise MJ.

Bioinformatics. 2012 Dec 1;28(23):3058-65. doi: 10.1093/bioinformatics/bts575. Epub 2012 Oct 8.

6.

Transient RNA structure features are evolutionarily conserved and can be computationally predicted.

Zhu JY, Steif A, Proctor JR, Meyer IM.

Nucleic Acids Res. 2013 Jul;41(12):6273-85. doi: 10.1093/nar/gkt319. Epub 2013 Apr 26.

7.

RNA folding during transcription: protocols and studies.

Wong TN, Pan T.

Methods Enzymol. 2009;468:167-93. doi: 10.1016/S0076-6879(09)68009-5.

PMID:
20946770
8.

Ab initio RNA folding.

Cragnolini T, Derreumaux P, Pasquali S.

J Phys Condens Matter. 2015 Jun 17;27(23):233102. doi: 10.1088/0953-8984/27/23/233102. Epub 2015 May 20. Review.

PMID:
25993396
9.

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.

Washietl S, Hofacker IL, Stadler PF, Kellis M.

Nucleic Acids Res. 2012 May;40(10):4261-72. doi: 10.1093/nar/gks009. Epub 2012 Jan 28.

10.

Regulatory effects of cotranscriptional RNA structure formation and transitions.

Liu SR, Hu CG, Zhang JZ.

Wiley Interdiscip Rev RNA. 2016 Sep;7(5):562-74. doi: 10.1002/wrna.1350. Epub 2016 Mar 29. Review.

PMID:
27028291
11.

Improving the accuracy of predicting secondary structure for aligned RNA sequences.

Hamada M, Sato K, Asai K.

Nucleic Acids Res. 2011 Jan;39(2):393-402. doi: 10.1093/nar/gkq792. Epub 2010 Sep 15.

12.

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

Meyer IM.

Methods. 2017 May 1;120:3-16. doi: 10.1016/j.ymeth.2017.04.009. Epub 2017 Apr 20. Review.

PMID:
28433606
13.

Concepts and introduction to RNA bioinformatics.

Gorodkin J, Hofacker IL, Ruzzo WL.

Methods Mol Biol. 2014;1097:1-31. doi: 10.1007/978-1-62703-709-9_1. Review.

PMID:
24639152
14.

Predicting folding pathways between RNA conformational structures guided by RNA stacks.

Li Y, Zhang S.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S5. doi: 10.1186/1471-2105-13-S3-S5.

15.

RNA folding during transcription.

Pan T, Sosnick T.

Annu Rev Biophys Biomol Struct. 2006;35:161-75. Review.

PMID:
16689632
16.

Interplay between single-stranded binding proteins on RNA secondary structure.

Lin YH, Bundschuh R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052707. Epub 2013 Nov 11.

PMID:
24329296
17.

RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies.

Yang XX, Deng ZL, Liu R.

Proteins. 2014 Oct;82(10):2455-71. doi: 10.1002/prot.24610. Epub 2014 Jun 9.

PMID:
24854765
18.

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.

Ding F, Sharma S, Chalasani P, Demidov VV, Broude NE, Dokholyan NV.

RNA. 2008 Jun;14(6):1164-73. doi: 10.1261/rna.894608. Epub 2008 May 2.

19.

Deleterious mutation prediction in the secondary structure of RNAs.

Barash D.

Nucleic Acids Res. 2003 Nov 15;31(22):6578-84.

20.

Exploiting structural and topological information to improve prediction of RNA-protein binding sites.

Maetschke SR, Yuan Z.

BMC Bioinformatics. 2009 Oct 18;10:341. doi: 10.1186/1471-2105-10-341.

Supplemental Content

Support Center