Structural inference of native and partially folded RNA by high-throughput contact mapping (Q36670098)

15 August 2017

Structural inference of native and partially folded RNA by high-throughput contact mapping (English)

1 reference

15 August 2017

Alain Laederach

4

0 references

Rhiju Das

object named as

Rhiju Das

1

0 references

David Baker

object named as

David Baker

7

0 references

Russ Altman

9

object named as

Russ B Altman

1 reference

15 August 2017

Madhuri Kudaravalli

2

1 reference

15 August 2017

Magdalena Jonikas

3

1 reference

15 August 2017

Robert Fong

5

1 reference

15 August 2017

Jason P Schwans

6

1 reference

15 August 2017

Joseph A Piccirilli

8

1 reference

15 August 2017

Daniel Herschlag

10

1 reference

15 August 2017

language of work or name

English

0 references

publication date

5 March 2008

1 reference

Proceedings of the National Academy of Sciences of the United States of America

15 August 2017

1 reference

15 August 2017

105

1 reference

15 August 2017

11

1 reference

15 August 2017

4144-4149

1 reference

Automated de novo prediction of native-like RNA tertiary structures

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Local RNA structural changes induced by crystallization are revealed by SHAPE

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Progress over the first decade of CASP experiments.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

RNA structure: reading the ribosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Ribosomal dynamics inferred from variations in experimental measurements

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Genetic control by metabolite-binding riboswitches

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

The global structure of the VS ribozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Mining biochemical information: lessons taught by the ribosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Rapid compaction during RNA folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Mechanism of ribosome recruitment by hepatitis C IRES RNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Multiple folding pathways for the P4-P6 RNA domain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Role of the molten globule state in protein folding.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Calculation of the relative geometry of tRNAs in the ribosome from directed hydroxyl-radical probing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

A chemogenetic approach to RNA function/structure analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

RNA folding causes secondary structure rearrangement

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Mechanical devices of the spliceosome: motors, clocks, springs, and things

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Hierarchy and dynamics of RNA folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Crystal structure of a group I ribozyme domain: principles of RNA packing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Visualization of RNA tertiary structure by RNA-EDTA.Fe(II) autocleavage: analysis of tRNA(Phe) with uridine-EDTA.Fe(II) at position 47

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Two major tertiary folding transitions of the Tetrahymena catalytic RNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Transcription termination in vitro at the tryptophan operon attenuator is controlled by secondary structures in the leader transcript

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Detailed molecular model for transfer ribonucleic acid

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

RNA structure and NMR spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Small angle X-ray scattering reveals a compact intermediate in RNA folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

The guanosine binding site of the Tetrahymena ribozyme

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

DNA and RNA sequence determination based on phosphorothioate chemistry

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

The paradoxical behavior of a highly structured misfolded intermediate in RNA folding.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2393762

Control of memory formation through regulated expression of a CaMKII transgene

20 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0709032105

Folding Mechanism of theTetrahymenaRibozyme P4−P6 Domain†

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0709032105

Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0709032105

Structural Requirement for Mg2+ Binding in the Group I Intron Core

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0709032105

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0709032105

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

21 January 2018

1 reference

12 December 2020

A magnesium ion core at the heart of a ribozyme domain

1 reference

12 December 2020

Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding

1 reference

12 December 2020

A collapsed non-native RNA folding state

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0709032105

1 reference

15 August 2017

0 references

1 reference

15 August 2017

PubMed publication ID

18322008

1 reference