Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain (Q37764842)

22 August 2017

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title

Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain (English)

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22 August 2017

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2

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Nikolay V. Dokholyan

series ordinal

3

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Christopher A Lavender

object named as

Christopher A Lavender

series ordinal

1

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author name string

Kevin M Weeks

series ordinal

4

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PMC publication ID

2889920

22 August 2017

language of work or name

English

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publication date

1 June 2010

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22 August 2017

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22 August 2017

49

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22 August 2017

24

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22 August 2017

4931-4933

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On the significance of an RNA tertiary structure prediction

22 August 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Toward a structural understanding of IRES RNA function

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

The pathway of hepatitis C virus mRNA recruitment to the human ribosome

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Comparison and functional implications of the 3D architectures of viral tRNA-like structures

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Structure and function of HCV IRES domains

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Viral IRES RNA structures and ribosome interactions

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

tRNA–mRNA mimicry drives translation initiation from a viral IRES

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Automated de novo prediction of native-like RNA tertiary structures

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Tertiary contacts distant from the active site prime a ribozyme for catalysis

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Mechanism of ribosome recruitment by hepatitis C IRES RNA

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

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

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Detection of tRNA-like Structure through RNase P Cleavage of Viral Internal Ribosome Entry Site RNAs Near the AUG Start Triplet

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Probing RNA structure with chemical reagents and enzymes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Structural basis for ribosome recruitment and manipulation by a viral IRES RNA.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

The pathway of HCV IRES-mediated translation initiation

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Specific cleavage of hepatitis C virus RNA genome by human RNase P.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889920

1 September 2018

Identifiers

DOI

10.1021/BI100142Y

1 reference

22 August 2017

1 reference

PMC publication ID

2889920

22 August 2017

PubMed publication ID

20545364

1 reference

PMC publication ID

2889920