Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics (Q34058315)

30 July 2017

title

Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics (English)

1 reference

30 July 2017

Allison J DePaul

1

1 reference

30 July 2017

Erik J Thompson

2

1 reference

30 July 2017

Sarav S Patel

3

1 reference

30 July 2017

Kristin Haldeman

4

1 reference

30 July 2017

Eric J Sorin

5

1 reference

30 July 2017

language of work or name

English

0 references

publication date

11 March 2010

1 reference

30 July 2017

number of pages

12

1 reference

based on heuristic

inferred from page(s)

published in

Nucleic Acids Research

1 reference

30 July 2017

volume

38

1 reference

30 July 2017

issue

14

1 reference

30 July 2017

page(s)

4856-4867

1 reference

Creative Commons Attribution-NonCommercial 2.5 Generic

30 July 2017

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Thermostat artifacts in replica exchange molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Annotation of tertiary interactions in RNA structures reveals variations and correlations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Side-chain recognition and gating in the ribosome exit tunnel.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Taking femtosecond snapshots of RNA conformational dynamics and complexity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Rearrangement of partially ordered stacked conformations contributes to the rugged energy landscape of a small RNA hairpin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Structural insight into RNA hairpin folding intermediates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Direct measurement of tertiary contact cooperativity in RNA 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=2919701

Recognition of a flipped base in a hairpinloop DNA by a small peptide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Is hairpin formation in single-stranded polynucleotide diffusion-controlled?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Does water play a structural role in the folding of small nucleic acids?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Structural Insight into the Antibiotic Action of Telithromycin against Resistant Mutants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Multiplexed-replica exchange molecular dynamics method for protein folding 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=2919701

Thermodynamic basis of the enhanced specificity of structured DNA probes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: evidence from Raman markers assignments.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Base dynamics in a UUCG tetraloop RNA hairpin characterized by 15N spin relaxation: correlations with structure and stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

A network of heterogeneous hydrogen bonds in GNRA tetraloops

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Solution structure of an ATP-binding RNA aptamer reveals a novel fold.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

VMD: visual molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Exceptionally stable nucleic acid hairpins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Bent helix formation between RNA hairpins with complementary loops

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

Tetraloops and RNA 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=2919701

Tertiary interactions determine the accuracy of RNA folding

5 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

Structural rearrangements linked to global folding pathways of the Azoarcus group I ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2919701

GROMACS 3.0: a package for molecular simulation and trajectory analysis

28 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

Crystal structure of the RNA component of bacterial ribonuclease P

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ134

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20223768

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20223768

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKQ134

1 reference

30 July 2017

1 reference

30 July 2017

1 reference