(Q34135131)

31 July 2017

title

ProbKnot: fast prediction of RNA secondary structure including pseudoknots (English)

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31 July 2017

1 reference

Stanislav Bellaousov

1

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31 July 2017

David H Mathews

series ordinal

2

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31 July 2017

language of work or name

English

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publication date

10 August 2010

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31 July 2017

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31 July 2017

volume

16

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31 July 2017

issue

10

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31 July 2017

page(s)

1870-1880

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RNAstructure: software for RNA secondary structure prediction and analysis

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Improved free energy parameters for RNA pseudoknotted secondary structure prediction

5 July 2018

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Improved RNA secondary structure prediction by maximizing expected pair accuracy

5 July 2018

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Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

5 July 2018

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Prediction of RNA secondary structure with pseudoknots using integer programming

5 July 2018

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Prediction of RNA secondary structure using generalized centroid estimators

5 July 2018

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Rfam: updates to the RNA families database

5 July 2018

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5 July 2018

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5 July 2018

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From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal

5 July 2018

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Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs

5 July 2018

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Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding

5 July 2018

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SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

CONTRAfold: RNA secondary structure prediction without physics-based models

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Prediction of RNA secondary structure by free energy minimization

5 July 2018

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Predicting RNA pseudoknot folding thermodynamics

5 July 2018

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Riboswitches as versatile gene control elements

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Asymmetry in RNA pseudoknots: observation and theory

5 July 2018

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Rfam: annotating non-coding RNAs in complete genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Pfold: RNA secondary structure prediction using stochastic context-free grammars

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Mfold web server for nucleic acid folding and hybridization prediction

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Rfam: an RNA family database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

The accuracy of ribosomal RNA comparative structure models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

The chemical repertoire of natural ribozymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Non–coding RNA genes and the modern RNA world

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

PseudoBase: structural information on RNA pseudoknots

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

RNA pseudoknot prediction in energy-based models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

The structural basis of ribosome activity in peptide bond synthesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Secondary structure of vertebrate telomerase RNA

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Comparative sequence analysis of tmRNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

A dynamic programming algorithm for RNA structure prediction including pseudoknots

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

The ribonuclease P database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Compilation of tRNA sequences and sequences of tRNA genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

A comparative database of group I intron structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Comparative and functional anatomy of group II catalytic introns—a review

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Prediction of RNA secondary structure, including pseudoknotting, by computer simulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Novel and efficient RNA secondary structure prediction using hierarchical folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Prediction of consensus RNA secondary structures including pseudoknots

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Prediction of locally stable RNA secondary structures for genome-wide surveys

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

A partition function algorithm for nucleic acid secondary structure including pseudoknots

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Equilibrium unfolding pathway of an H-type RNA pseudoknot which promotes programmed -1 ribosomal frameshifting

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

An RNA folding method capable of identifying pseudoknots and base triples

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

The computer simulation of RNA folding pathways using a genetic algorithm.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

RNA pseudoknots. Stability and loop size requirements

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941096

Equilibrium unfolding (folding) pathway of a model H-type pseudoknotted RNA: the role of magnesium ions in stability

28 October 2018

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12 December 2020

Thermodynamics of three-way multibranch loops in RNA

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12 December 2020

tmRDB (tmRNA database)

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12 December 2020

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing — a review

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12 December 2020

The Signal Recognition Particle Database (SRPDB)

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12 December 2020

Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot

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12 December 2020

Identifiers

DOI

10.1261/RNA.2125310

1 reference

31 July 2017

1 reference

31 July 2017

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