Literature DB >> 18428968

RNA secondary structure prediction.

David H Mathews1, Douglas H Turner, Michael Zuker.   

Abstract

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.

Entities:  

Mesh：

Substances：

Year:  2007        PMID： 18428968      PMCID： PMC5115178          DOI： 10.1002/0471142700.nc1102s28

Source DB:  PubMed          Journal:  Curr Protoc Nucleic Acid Chem        ISSN： 1934-9270


  29 in total

1.  Predicting oligonucleotide affinity to nucleic acid targets.

Authors:  D H Mathews; M E Burkard; S M Freier; J R Wyatt; D H Turner
Journal:  RNA       Date:  1999-11       Impact factor: 4.942

2.  Using reliability information to annotate RNA secondary structures.

Authors:  M Zuker; A B Jacobson
Journal:  RNA       Date:  1998-06       Impact factor: 4.942

3.  Phylogenetic analysis of tmRNA secondary structure.

Authors:  K P Williams; D P Bartel
Journal:  RNA       Date:  1996-12       Impact factor: 4.942

4.  The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript.

Authors:  Erin A Bohula; Amanda J Salisbury; Muhammad Sohail; Martin P Playford; Johann Riedemann; Edwin M Southern; Valentine M Macaulay
Journal:  J Biol Chem       Date:  2003-02-24       Impact factor: 5.157

5.  Thermodynamic criteria for high hit rate antisense oligonucleotide design.

Authors:  O V Matveeva; D H Mathews; A D Tsodikov; S A Shabalina; R F Gesteland; J F Atkins; S M Freier
Journal:  Nucleic Acids Res       Date:  2003-09-01       Impact factor: 16.971

6.  Messenger RNA expression profiling of genes involved in epidermal growth factor receptor signalling in human cancer cells treated with scanning array-designed antisense oligonucleotides.

Authors:  Amelia K Petch; Muhammad Sohail; Marcus D Hughes; Ibrahim Benter; John Darling; Edwin M Southern; Saghir Akhtar
Journal:  Biochem Pharmacol       Date:  2003-09-01       Impact factor: 5.858

7.  Enzymatic approaches to probing of RNA secondary and tertiary structure.

Authors:  G Knapp
Journal:  Methods Enzymol       Date:  1989       Impact factor: 1.600

8.  Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

Authors:  Robin D Dowell; Sean R Eddy
Journal:  BMC Bioinformatics       Date:  2004-06-04       Impact factor: 3.169

9.  Compilation of tRNA sequences and sequences of tRNA genes.

Authors:  Mathias Sprinzl; Konstantin S Vassilenko
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

10.  siRNA target site secondary structure predictions using local stable substructures.

Authors:  Bret S E Heale; Harris S Soifer; Chauncey Bowers; John J Rossi
Journal:  Nucleic Acids Res       Date:  2005-02-18       Impact factor: 16.971
View more
  36 in total

1.  Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells.

Authors:  Irina E Catrina; Salvatore A E Marras; Diana P Bratu
Journal:  ACS Chem Biol       Date:  2012-07-06       Impact factor: 5.100

2.  Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.

Authors:  William M Rockey; Frank J Hernandez; Sheng-You Huang; Song Cao; Craig A Howell; Gregory S Thomas; Xiu Ying Liu; Natalia Lapteva; David M Spencer; James O McNamara; Xiaoqin Zou; Shi-Jie Chen; Paloma H Giangrande
Journal:  Nucleic Acid Ther       Date:  2011-10       Impact factor: 5.486

3.  HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs.

Authors:  Sylvanne M Daniels; Lucile Sinck; Natalie J Ward; Carlos E Melendez-Peña; Robert J Scarborough; Ibrahim Azar; Elodie Rance; Aïcha Daher; Ka-Ming Pang; John J Rossi; Anne Gatignol
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

4.  Accurate SHAPE-directed RNA structure determination.

Authors:  Katherine E Deigan; Tian W Li; David H Mathews; Kevin M Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-24       Impact factor: 11.205

5.  The microRNAs of Epstein-Barr Virus are expressed at dramatically differing levels among cell lines.

Authors:  Zachary L Pratt; Malika Kuzembayeva; Srikumar Sengupta; Bill Sugden
Journal:  Virology       Date:  2009-02-12       Impact factor: 3.616

Review 6.  Decoding mechanisms by which silent codon changes influence protein biogenesis and function.

Authors:  Vedrana Bali; Zsuzsanna Bebok
Journal:  Int J Biochem Cell Biol       Date:  2015-03-26       Impact factor: 5.085

7.  Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy.

Authors:  Chi H Mak; Tyler Matossian; Wen-Yeuan Chung
Journal:  Biophys J       Date:  2014-04-01       Impact factor: 4.033

8.  Interaction between thymidylate synthase and its cognate mRNA in zebrafish embryos.

Authors:  Yuyan Zhang; Shaoli Yang; Ming Liu; Chunxia Song; Ning Wu; Peixue Ling; Edward Chu; Xiukun Lin
Journal:  PLoS One       Date:  2010-05-12       Impact factor: 3.240

9.  Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays.

Authors:  Ranjit Kumar; Pratik Shah; Edwin Swiatlo; Shane C Burgess; Mark L Lawrence; Bindu Nanduri
Journal:  BMC Genomics       Date:  2010-06-03       Impact factor: 3.969

10.  B7-H4 gene polymorphisms are associated with sporadic breast cancer in a Chinese Han population.

Authors:  Jie Zhang; Mingyan Zhang; Wei Jiang; Lihong Wang; Zhenkun Fu; Dalin Li; Da Pang; Dianjun Li
Journal:  BMC Cancer       Date:  2009-11-11       Impact factor: 4.430
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.