(Q30572845)

21 August 2017

Differences between cotranscriptional and free riboswitch folding (English)

1 reference

21 August 2017

Stefan Klumpp

4

0 references

author name string

Benjamin Lutz

1

1 reference

21 August 2017

Michael Faber

2

1 reference

21 August 2017

Abhinav Verma

3

1 reference

21 August 2017

Alexander Schug

5

1 reference

21 August 2017

language of work or name

English

0 references

publication date

25 November 2013

1 reference

21 August 2017

Nucleic Acids Research

1 reference

21 August 2017

42

1 reference

21 August 2017

4

1 reference

21 August 2017

2687-2696

1 reference

Creative Commons Attribution 3.0 Unported

21 August 2017

start time

10 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Direct observation of cotranscriptional folding in an adenine riboswitch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Cooperative tertiary interaction network guides RNA folding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Chain length determines the folding rates of RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Excited states of ribosome translocation revealed through integrative molecular modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Riboswitch structure in the ligand-free state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Cooperative and directional folding of the preQ1 riboswitch aptamer domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

From protein folding to protein function and biomolecular binding by energy landscape theory

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Ribozymes and riboswitches: modulation of RNA function by small molecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Elongation by RNA polymerase: a race through roadblocks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

RNA polymerase active center: the molecular engine of transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

RNA polymerase: the vehicle of transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

The distributions, mechanisms, and structures of metabolite-binding riboswitches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Mutations as trapdoors to two competing native conformations of the Rop-dimer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Folding of the adenine riboswitch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Thinking quantitatively about transcriptional regulation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Theory of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Sensing Small Molecules by Nascent RNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Maximizing RNA folding rates: a balancing act.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

RNA folding at elementary step resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

RNA polymerase slides home: pause and termination site recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3936736

The kinetics of ligand binding by an adenine-sensing riboswitch

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

Size, shape, and flexibility of RNA structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

Robustness and generalization of structure-based models for protein folding and function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

Topological frustration and the folding of interleukin-1 beta

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

Origin of life: The RNA world

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1213

The dynamic nature of RNA as key to understanding riboswitch mechanisms

21 January 2018

1 reference

12 December 2020

Coupled dynamics of RNA folding and nanopore translocation

1 reference

12 December 2020

Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails

1 reference

12 December 2020

Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKT1213

1 reference

21 August 2017

1 reference

21 August 2017

PubMed publication ID

24275497

1 reference