Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure. (Q35623931)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21889515%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

title

Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure (English)

1 reference

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12 February 2020

0 references

2

1 reference

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12 February 2020

Robin Gutell

series ordinal

4

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12 February 2020

author name string

David P Gardner

series ordinal

1

1 reference

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12 February 2020

Stuart Ozer

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3

1 reference

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12 February 2020

language of work or name

English

0 references

publication date

23 August 2011

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Journal of Molecular Biology

12 February 2020

published in

1 reference

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12 February 2020

volume

413

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12 February 2020

issue

2

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12 February 2020

page(s)

473-483

1 reference

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Computational approaches for RNA energy parameter estimation

12 February 2020

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12 July 2018

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Thermodynamic characterization of naturally occurring RNA tetraloops

12 July 2018

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12 July 2018

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Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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12 July 2018

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Statistical potential for assessment and prediction of protein structures

12 July 2018

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The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits

12 July 2018

1 reference

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CONTRAfold: RNA secondary structure prediction without physics-based models

12 July 2018

1 reference

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Progress over the first decade of CASP experiments.

12 July 2018

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A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

12 July 2018

1 reference

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Extracting stacking interaction parameters for RNA from the data set of native structures

12 July 2018

1 reference

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Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

12 July 2018

1 reference

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Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2.

12 July 2018

1 reference

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

12 July 2018

1 reference

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Secondary structure models of the 3' untranslated regions of diverse R2 RNAs

12 July 2018

1 reference

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242814

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

12 July 2018

1 reference

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The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy

12 July 2018

1 reference

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Vienna RNA secondary structure server

12 July 2018

1 reference

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Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

12 July 2018

1 reference

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SRPDB: Signal Recognition Particle Database

12 July 2018

1 reference

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The accuracy of ribosomal RNA comparative structure models

12 July 2018

1 reference

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The hepatitis C virus internal ribosome-entry site: a new target for antiviral research

12 July 2018

1 reference

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The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

12 July 2018

1 reference

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A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria

12 July 2018

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The energetics of small internal loops in RNA.

12 July 2018

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

12 July 2018

1 reference

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The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria

12 July 2018

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12 July 2018

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

12 July 2018

1 reference

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The structural basis of hammerhead ribozyme self-cleavage

12 July 2018

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Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress

12 July 2018

1 reference

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The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures

12 July 2018

1 reference

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Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces

12 July 2018

1 reference

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A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242814

Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242814

Comparative anatomy of 16-S-like ribosomal RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242814

Improved predictions of secondary structures for RNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242814

On finding all suboptimal foldings of an RNA molecule

12 July 2018

1 reference

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CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes

12 July 2018

1 reference

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Improved free-energy parameters for predictions of RNA duplex stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242814

Structure and replication of the genome of the hepatitis delta virus

12 July 2018

1 reference

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Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains both universal and yeast-specific domains

12 July 2018

1 reference

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Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

12 July 2018

1 reference

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Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"

12 July 2018

1 reference

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A thermodynamic study of unusually stable RNA and DNA hairpins

12 July 2018

1 reference

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Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops

12 July 2018

1 reference

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Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

12 July 2018

1 reference

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The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA.

12 July 2018

1 reference

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A story: unpaired adenosine bases in ribosomal RNAs

25 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21889515

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Thermodynamics of three-way multibranch loops in RNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21889515

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The stability and structure of tandem GA mismatches in RNA depend on closing base pairs

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21889515

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JMB.2011.08.033

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21889515%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21889515%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

PubMed publication ID

21889515

1 reference