(Q30884437)

19 September 2017

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets (English)

1 reference

molecular dynamics simulation

19 September 2017

0 references

1 reference

4

1 reference

19 September 2017

Jirí Sponer

5

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author name string

Kamila Réblová

series ordinal

1

1 reference

19 September 2017

Nad'a Spacková

series ordinal

2

1 reference

19 September 2017

Judit E Sponer

series ordinal

3

1 reference

19 September 2017

language of work or name

English

0 references

publication date

1 December 2003

1 reference

19 September 2017

Nucleic Acids Research

1 reference

19 September 2017

31

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19 September 2017

23

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19 September 2017

6942-6952

1 reference

Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

A crystallographic study of the binding of 13 metal ions to two related RNA duplexes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Molecular dynamics applied to nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Simulations of nucleic acids and their complexes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Cooperativity in drug-DNA recognition: a molecular dynamics study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Structure and dimerization of HIV-1 kissing loop aptamers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

A retroviral RNA kissing complex containing only two G⋅C base pairs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Molecular dynamics simulations of solvated yeast tRNA(Asp).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

The solution structure of an RNA loop-loop complex: the ColE1 inverted loop sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Structure of the dimer initiation complex of HIV-1 genomic RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

VMD: visual molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Antisense RNA control in bacteria, phages, and plasmids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Mapping of poly(A) sequences in the electron microscope reveals unusual structure of type C oncornavirus RNA molecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

The linkage between magnesium binding and RNA folding.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=290250

Molecular dynamics investigations of hammerhead ribozyme RNA

25 November 2018

1 reference

12 December 2020

RNA solvation: a molecular dynamics simulation perspective

1 reference

12 December 2020

Molecular modeling and dynamics studies of HIV-1 kissing loop structures

1 reference

12 December 2020

Structure of the Sm binding site from human U4 snRNA derived from a 3 ns PME molecular dynamics simulation

1 reference

12 December 2020

A molecular dynamics simulation study of coaxial stacking in RNA

1 reference

12 December 2020

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

1 reference

12 December 2020

Crystallographic refinement of yeast aspartic acid transfer RNA

1 reference

12 December 2020

Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation

1 reference

12 December 2020

A kissing complex together with a stable dimer is involved in the HIV-1Lai RNA dimerization process in vitro

1 reference

12 December 2020

Dimerization of MoMuLV genomic RNA: redefinition of the role of the palindromic stem-loop H1 (278-303) and new roles for stem-loops H2 (310-352) and H3 (355-374)

1 reference

12 December 2020

Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKG880

1 reference

19 September 2017

1 reference

19 September 2017

1 reference