RNA secondary structure prediction (Q37422746)

20 August 2017

RNA secondary structure prediction (English)

1 reference

20 August 2017

2

Douglas H Turner

1 reference

20 August 2017

David H Mathews

1

1 reference

PMCID

5115178

20 August 2017

Michael Zuker

series ordinal

3

1 reference

20 August 2017

1 March 2007

1 reference

Current protocols in nucleic acid chemistry / editorial board, Serge L. Beaucage ... [et al.]

20 August 2017

1 reference

20 August 2017

Chapter 11

1 reference

20 August 2017

Unit 11.2

1 reference

ProbKnot: fast prediction of RNA secondary structure including pseudoknots

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Improved RNA secondary structure prediction by maximizing expected pair accuracy

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Accurate SHAPE-directed RNA structure determination

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Efficient siRNA selection using hybridization thermodynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

siRNA target site secondary structure predictions using local stable substructures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Compilation of tRNA sequences and sequences of tRNA genes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

How do RNA folding algorithms work?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Vienna RNA secondary structure server

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Predicting oligonucleotide affinity to nucleic acid targets

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

A dynamic programming algorithm for RNA structure prediction including pseudoknots

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

The Ribonuclease P Database

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Using reliability information to annotate RNA secondary structures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Phylogenetic analysis of tmRNA secondary structure.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

"Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

On finding all suboptimal foldings of an RNA molecule

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Probing the structure of RNAs in solution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

Thermodynamic criteria for high hit rate antisense oligonucleotide design

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5115178

A partition function algorithm for nucleic acid secondary structure including pseudoknots

14 September 2017

1 reference

Crossref

https://api.crossref.org/works/10.1002%2F0471142700.NC1102S28

Enzymatic approaches to probing of RNA secondary and tertiary structure

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18428968

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18428968

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/0471142700.NC1102S28

1 reference

20 August 2017

1 reference

20 August 2017

1 reference

PMCID

5115178