Clustering to identify RNA conformations constrained by secondary structure (Q34621190)

3 August 2017

title

Clustering to identify RNA conformations constrained by secondary structure (English)

1 reference

3 August 2017

2

Michael Levitt

1 reference

3 August 2017

Adelene Y L Sim

1

1 reference

3 August 2017

language of work or name

English

0 references

publication date

11 February 2011

1 reference

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

3 August 2017

published in

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3 August 2017

volume

108

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3 August 2017

issue

9

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3 August 2017

page(s)

3590-3595

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Computational approaches to 3D modeling of RNA.

3 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=3048103

Turning limited experimental information into 3D models of RNA

7 July 2018

1 reference

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On the significance of an RNA tertiary structure prediction

7 July 2018

1 reference

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Atomic accuracy in predicting and designing noncanonical RNA structure

7 July 2018

1 reference

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The ligand-free state of the TPP riboswitch: a partially folded RNA structure

7 July 2018

1 reference

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Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

7 July 2018

1 reference

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Progress and challenges in the automated construction of Markov state models for full protein systems

7 July 2018

1 reference

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Tertiary motifs revealed in analyses of higher-order RNA junctions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Analysis of four-way junctions in RNA structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

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

7 July 2018

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Riboswitches: emerging themes in RNA structure and function

7 July 2018

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Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

7 July 2018

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Ligand-dependent folding of the three-way junction in the purine riboswitch

7 July 2018

1 reference

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RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign

7 July 2018

1 reference

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Automated de novo prediction of native-like RNA tertiary structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain

7 July 2018

1 reference

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Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Growth of novel protein structural data.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Folding of the adenine riboswitch

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

RNA folding during transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

The folding of the hairpin ribozyme: dependence on the loops and the junction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Tertiary Motifs in RNA Structure and Folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Clustering of low-energy conformations near the native structures of small proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Hierarchy and dynamics of RNA folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048103

Topology of three-way junctions in folded RNAs

7 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018653108

Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018653108

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018653108

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018653108

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21317361

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21317361

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Modeling Unusual Nucleic Acid Structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1073/PNAS.1018653108

Identifiers

DOI

10.1073/PNAS.1018653108

1 reference

3 August 2017

0 references

1 reference

3 August 2017

1 reference