(Q35775755)

10 August 2017

title

Improved prediction of RNA tertiary structure with insights into native state dynamics (English)

1 reference

10 August 2017

John Paul Bida

1

1 reference

10 August 2017

L James Maher

series ordinal

2

1 reference

10 August 2017

language of work or name

English

0 references

publication date

25 January 2012

1 reference

10 August 2017

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10 August 2017

volume

18

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10 August 2017

issue

3

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10 August 2017

page(s)

385-393

1 reference

ModeRNA: a tool for comparative modeling of RNA 3D structure

10 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=3285927

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Atomic accuracy in predicting and designing noncanonical RNA 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=3285927

VORO++: a three-dimensional voronoi cell library in C++.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Predicting RNA structure by multiple template homology modeling

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

CENTROIDFOLD: a web server for RNA secondary structure 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=3285927

A sequence element that tunes Escherichia coli tRNA(Ala)(GGC) to ensure accurate decoding.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Prediction of RNA secondary structure using generalized centroid estimators

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

iFoldRNA: three-dimensional RNA structure prediction and folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of 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=3285927

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

DNA mimicry by a high-affinity anti-NF- B RNA aptamer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Automated de novo prediction of native-like RNA tertiary structures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

CONTRAfold: RNA secondary structure prediction without physics-based models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Describing RNA structure by libraries of clustered nucleotide doublets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to 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=3285927

The structure-function dilemma of the hammerhead ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

The application of cluster analysis in the intercomparison of loop structures in 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=3285927

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Molecular mimicry of the NF-kappaB DNA target site by a selected RNA aptamer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Crystal structure of NF- B (p50)2 complexed to a high-affinity RNA aptamer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Selection and characterization of an RNA decoy for transcription factor NF-kappa B.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Topology links RNA secondary structure with global conformation, dynamics, and adaptation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

NMR-spectroscopic characterization of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

Predicting RNA secondary structures with pseudoknots by MCMC sampling.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3285927

In vivo recognition of an RNA aptamer by its transcription factor target

25 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22279150

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Binding stoichiometry of an RNA aptamer and its transcription factor target

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22279150

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A story: unpaired adenosine bases in ribosomal RNAs

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22279150

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.027201.111

1 reference

10 August 2017

1 reference

10 August 2017

1 reference