Computational approaches for RNA energy parameter estimation (Q34370079)

1 August 2017

title

Computational approaches for RNA energy parameter estimation (English)

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1 August 2017

1 reference

Holger H Hoos

3

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Anne Condon

series ordinal

2

object named as

Anne Condon

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1 August 2017

Mirela Andronescu

1

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1 August 2017

David H Mathews

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4

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1 August 2017

Kevin P Murphy

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5

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1 August 2017

language of work or name

English

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publication date

12 October 2010

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1 August 2017

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1 August 2017

volume

16

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1 August 2017

issue

12

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1 August 2017

page(s)

2304-2318

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Improved free energy parameters for RNA pseudoknotted secondary structure prediction

1 August 2017

cites work

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6 July 2018

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6 July 2018

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NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon

6 July 2018

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A max-margin model for efficient simultaneous alignment and folding of RNA sequences

6 July 2018

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High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

6 July 2018

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6 July 2018

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6 July 2018

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Efficient siRNA selection using hybridization thermodynamics

6 July 2018

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Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

6 July 2018

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6 July 2018

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Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

6 July 2018

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Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting

6 July 2018

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NMR Structures of (rGC U GA G GCU) 2 and (rGC G GA U GCU) 2 : Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs † , ‡

6 July 2018

1 reference

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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

6 July 2018

1 reference

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

6 July 2018

1 reference

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CONTRAfold: RNA secondary structure prediction without physics-based models

6 July 2018

1 reference

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Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

6 July 2018

1 reference

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Consecutive GA pairs stabilize medium-size RNA internal loops

6 July 2018

1 reference

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Statistical and Bayesian approaches to RNA secondary structure prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Computational models with thermodynamic and composition features improve siRNA design

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

The tmRDB and SRPDB resources

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamics of RNA duplexes with tandem mismatches containing a uracil-uracil pair flanked by C.G/G.C or G.C/A.U closing base pairs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Stability of 3' double nucleotide overhangs that model the 3' ends of siRNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Solution structure of an RNA internal loop with three consecutive sheared GA pairs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Fast and reliable prediction of noncoding RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Compilation of tRNA sequences and sequences of tRNA genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Fast and effective prediction of microRNA/target duplexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Pronounced instability of tandem IU base pairs in RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Identification of many microRNAs that copurify with polyribosomes in mammalian neurons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

A statistical sampling algorithm for RNA secondary structure prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Tools for the automatic identification and classification of RNA base pairs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Mfold web server for nucleic acid folding and hybridization prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

The Protein Data Bank and structural genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Identification of novel genes coding for small expressed RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Structural diversity of self-cleaving ribozymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

A test of the model to predict unusually stable RNA hairpin loop stability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

RNA folding at elementary step resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Predicting oligonucleotide affinity to nucleic acid targets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

RNAs that bind and change the permeability of phospholipid membranes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Complete suboptimal folding of RNA and the stability of secondary structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamics of RNA hairpins containing single internal mismatches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

The Ribonuclease P Database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

RNA hairpin loop stability depends on closing base pair

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

A periodic table of symmetric tandem mismatches in RNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Purine-purine mismatches in RNA helices: evidence for protonated G.A pairs and next-nearest neighbor effects

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Improved Estimation of Secondary Structure in Ribonucleic Acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Characterization of RNA hairpin loop stability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Phylogenetic comparative analysis of RNA secondary structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

On finding all suboptimal foldings of an RNA molecule

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

A thermodynamic study of unusually stable RNA and DNA hairpins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Simulating RNA folding kinetics on approximated energy landscapes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Folding kinetics of large RNAs

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic characterization of single mismatches found in naturally occurring RNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Efficient parameter estimation for RNA secondary structure prediction

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

RNAshapes: an integrated RNA analysis package based on abstract shapes

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Programmable ligand-controlled riboregulators of eukaryotic gene expression

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Secondary structure prediction of interacting RNA molecules

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Stability of RNA hairpin loops closed by AU base pairs

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamic stabilities of internal loops with GU closing pairs in RNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2995392

Free energy contributions of G.U and other terminal mismatches to helix stability

27 October 2018

1 reference

12 December 2020

Energetics of internal GU mismatches in ribooligonucleotide helixes

1 reference

12 December 2020

Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid

1 reference

12 December 2020

Effects of GA mismatches on the structure and thermodynamics of RNA internal loops

1 reference

12 December 2020

Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C. pairs

1 reference

12 December 2020

Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]

1 reference

12 December 2020

A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides

1 reference

12 December 2020

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

1 reference

12 December 2020

Thermodynamics of single mismatches in RNA duplexes

1 reference

12 December 2020

Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA

1 reference

12 December 2020

Thermodynamics of three-way multibranch loops in RNA

1 reference

12 December 2020

G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides

1 reference

12 December 2020

Improved parameters for the prediction of RNA hairpin stability

1 reference

12 December 2020

Thermodynamics of Nonsymmetric Tandem Mismatches Adjacent to G·C Base Pairs in RNA

1 reference

12 December 2020

Stability of RNA Hairpins Closed by Wobble Base Pairs

1 reference

12 December 2020

Measuring the thermodynamics of RNA secondary structure formation

1 reference

12 December 2020

Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns

1 reference

12 December 2020

Thermodynamic characterization of RNA duplexes containing naturally occurring 1 x 2 nucleotide internal loops

1 reference

12 December 2020

Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches

1 reference

12 December 2020

Identifiers

DOI

10.1261/RNA.1950510

1 reference

release_b3ugc5c5ifdurico3uo4ke5h6i

1 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/b3ugc5c5ifdurico3uo4ke5h6i

24 November 2022

mapped directly with Wikidata item

PMC publication ID

2995392

1 reference

1 August 2017

1 reference