(Q35646838)

9 August 2017

title

High sensitivity RNA pseudoknot prediction (English)

1 reference

9 August 2017

Xiaolu Huang

1

1 reference

9 August 2017

Hesham Ali

series ordinal

2

1 reference

9 August 2017

language of work or name

English

0 references

publication date

19 December 2006

1 reference

9 August 2017

published in

Nucleic Acids Research

1 reference

9 August 2017

volume

35

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9 August 2017

issue

2

1 reference

9 August 2017

page(s)

656-663

1 reference

Predicting RNA pseudoknot folding thermodynamics

9 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Asymmetry in RNA pseudoknots: observation and theory

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Torsional restraint: a new twist on frameshifting pseudoknots

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Vienna RNA secondary structure server

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Mfold web server for nucleic acid folding and hybridization prediction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

PseudoBase: a database with RNA pseudoknots

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

A dynamic programming algorithm for RNA structure prediction including pseudoknots

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Recoding: dynamic reprogramming of translation.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

A general method applicable to the search for similarities in the amino acid sequence of two proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

Structural and functional aspects of RNA pseudoknots

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1802631

An RNA folding method capable of identifying pseudoknots and base triples.

12 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL943

A partition function algorithm for nucleic acid secondary structure including pseudoknots

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL943

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL943

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL943

An approximation of loop free energy values of RNA H-pseudoknots

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL943

Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17179177

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Thermodynamics of folding a pseudoknotted mRNA fragment

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17179177

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL943

1 reference

9 August 2017

1 reference

9 August 2017

1 reference