Molecular dynamics simulations of RNA: an in silico single molecule approach. (Q36058510)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17080418%20AND%20SRC:MED&resulttype=core&format=json

21 December 2019

review article

1 reference

title

Molecular dynamics simulations of RNA: an in silico single molecule approach (English)

1 reference

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21 December 2019

1 reference

3

1 reference

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21 December 2019

Nils G Walter

series ordinal

4

1 reference

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21 December 2019

author name string

S Elizabeth McDowell

series ordinal

1

1 reference

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21 December 2019

Nad'a Spacková

series ordinal

2

1 reference

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21 December 2019

publication date

1 February 2007

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21 December 2019

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21 December 2019

volume

85

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21 December 2019

issue

2

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21 December 2019

page(s)

169-184

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The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

21 December 2019

cites work

1 reference

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Trapped water molecules are essential to structural dynamics and function of a ribozyme

2 October 2017

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When to believe what you see.

2 October 2017

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2 October 2017

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

2 October 2017

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2 October 2017

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2 October 2017

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Characterization of the piRNA Complex from Rat Testes

2 October 2017

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Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations

2 October 2017

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2 October 2017

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The principles of guiding by RNA: chimeric RNA-protein enzymes

2 October 2017

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Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

2 October 2017

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Molecular dynamics simulations of the complete satellite tobacco mosaic virus

2 October 2017

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Structural and evolutionary classification of G/U wobble basepairs in the ribosome

2 October 2017

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Molecular dynamics simulations of sarcin-ricin rRNA motif.

2 October 2017

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Hfq variant with altered RNA binding functions

2 October 2017

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Chemical biology at the crossroads of molecular structure and mechanism

2 October 2017

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The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA

2 October 2017

1 reference

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Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study

2 October 2017

1 reference

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Insights on HIV-1 Tat:P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations.

2 October 2017

1 reference

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2 October 2017

MicroRNAs as oncogenes

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Simulating movement of tRNA into the ribosome during decoding

2 October 2017

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E. coli RNase HI and the phosphonate-DNA/RNA hybrid: molecular dynamics simulations.

2 October 2017

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Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study

2 October 2017

1 reference

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Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference

2 October 2017

1 reference

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Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study

2 October 2017

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Mechanisms of X-chromosome inactivation

2 October 2017

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A strategy for probing the function of noncoding RNAs finds a repressor of NFAT

2 October 2017

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Ribo-gnome: the big world of small RNAs

2 October 2017

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Mechanism of peptide bond synthesis on the ribosome

2 October 2017

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Comparison of mode analyses at different resolutions applied to nucleic acid systems

2 October 2017

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In vivo application of RNA interference: from functional genomics to therapeutics

2 October 2017

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Silence from within: endogenous siRNAs and miRNAs.

2 October 2017

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Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif

2 October 2017

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An abundance of RNA regulators

2 October 2017

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Exploring global motions and correlations in the ribosome

2 October 2017

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2 October 2017

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Post-transcriptional gene silencing by siRNAs and miRNAs

2 October 2017

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Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution

2 October 2017

1 reference

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Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

2 October 2017

1 reference

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

2 October 2017

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Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern †

2 October 2017

1 reference

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Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations

2 October 2017

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Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations

2 October 2017

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Opening mechanism of G.T/U pairs in DNA and RNA duplexes: a combined study of imino proton exchange and molecular dynamics simulation

2 October 2017

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siRNA therapeutics: big potential from small RNAs

2 October 2017

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Ion motions in molecular dynamics simulations on DNA.

2 October 2017

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Unlocking the potential of the human genome with RNA interference

2 October 2017

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Mechanisms of gene silencing by double-stranded RNA

2 October 2017

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Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex

2 October 2017

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DNA and its counterions: a molecular dynamics study

2 October 2017

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Nucleic acid transport through carbon nanotube membranes

2 October 2017

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Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

2 October 2017

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MicroRNAs: small RNAs with a big role in gene regulation

2 October 2017

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Simulation and modeling of nucleic acid structure, dynamics and interactions

2 October 2017

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Viroids: the minimal non-coding RNAs with autonomous replication

2 October 2017

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On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV-1 in solution: a molecular dynamics simulation and electrophoresis study

2 October 2017

1 reference

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siRNAs: applications in functional genomics and potential as therapeutics

2 October 2017

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MD studies of the DIS/DIS kissing complex solution and x-ray structures

2 October 2017

1 reference

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Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations.

2 October 2017

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Molecular dynamics simulation of hepatitis C virus IRES IIId domain: structural behavior, electrostatic and energetic analysis

2 October 2017

1 reference

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Effect of G-1 on histidine tRNA microhelix conformation

2 October 2017

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Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

2 October 2017

1 reference

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Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations

2 October 2017

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

2 October 2017

1 reference

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The base sequence dependent flexibility of linear single-stranded oligoribonucleotides correlates with the reactivity of the phosphodiester bond

2 October 2017

1 reference

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Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

2 October 2017

1 reference

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Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

2 October 2017

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The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop base pair

2 October 2017

1 reference

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

2 October 2017

1 reference

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Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis

2 October 2017

1 reference

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

2 October 2017

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The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications

2 October 2017

1 reference

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Mutations proximal to the minor groove-binding track of human immunodeficiency virus type 1 reverse transcriptase differentially affect utilization of RNA versus DNA as template

2 October 2017

1 reference

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Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations

2 October 2017

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The solution structure of the loop E region of the 5S rRNA from spinach chloroplasts

2 October 2017

1 reference

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Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration

2 October 2017

1 reference

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HIV-1(Lai) genomic RNA: combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin

2 October 2017

1 reference

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The non-Watson-Crick base pairs and their associated isostericity matrices

2 October 2017

1 reference

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Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study

2 October 2017

1 reference

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Catalytic strategies of the hepatitis delta virus ribozymes

2 October 2017

1 reference

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The kink-turn: a new RNA secondary structure motif

2 October 2017

1 reference

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Imino proton exchange and base-pair kinetics in RNA duplexes

2 October 2017

1 reference

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Molecular dynamics simulation of the human U2B" protein complex with U2 snRNA hairpin IV in aqueous solution

2 October 2017

1 reference

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Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex

2 October 2017

1 reference

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Crystal structure of the ribosome at 5.5 A resolution

2 October 2017

1 reference

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

2 October 2017

1 reference

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

2 October 2017

1 reference

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2 October 2017

The Protein Data Bank

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A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics simulations of solvated yeast tRNA(Asp).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

A computational approach to the mechanism of self-cleavage of hammerhead RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

General acid catalysis by the hepatitis delta virus ribozyme

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Dynamics and stability of GCAA tetraloops with 2-aminopurine and purine substitutions

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

A conformational switch controls hepatitis delta virus ribozyme catalysis

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Base pairing at the stem-loop junction in the SL1 kissing complex of HIV-1 RNA: a thermodynamic study probed by molecular dynamics simulation.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Altering the RNA-binding mode of the U1A RBD1 protein

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Conformational flexibility of two RNA trimers explored by computational tools and database search

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics and thermodynamics of protein-RNA interactions: mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Molecular dynamics studies of U1A-RNA complexes

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2018183

Simulation of the structure and dynamics of nonhelical RNA motifs

23 September 2018

1 reference

12 December 2020

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

1 reference

12 December 2020

Structural basis for the unusual properties of 2',5' nucleic acids and their complexes with RNA and DNA

1 reference

12 December 2020

Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?

1 reference

12 December 2020

Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs

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

The molecular dynamics thermocycler. A new approach to sample conformational space, as exemplified by the RNA hairpin

1 reference

12 December 2020

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

1 reference

12 December 2020

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

1 reference

12 December 2020

Structure, Recognition Properties, and Flexibility of the DNA·RNA Hybrid

1 reference

12 December 2020

Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita

1 reference

12 December 2020

Dynamics of the native and the ligand-bound structures of eosinophil cationic protein: network of hydrogen bonds at the catalytic site

1 reference

12 December 2020

Conformational pathway for the kissing complex-->extended dimer transition of the SL1 stem-loop from genomic HIV-1 RNA as monitored by targeted molecular dynamics techniques

1 reference

12 December 2020

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

1 reference

12 December 2020

Structure and dynamics of RNA polymerase II elongation complex

1 reference

12 December 2020

Principles of RNA Base Pairing: Structures and Energies of the Trans Watson−Crick/Sugar Edge Base Pairs

1 reference

12 December 2020

Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA

1 reference

12 December 2020

Role of Solvent Dynamics in Stabilizing the Transition State of RNA Hydrolysis by Hairpin Ribozyme.

1 reference

12 December 2020

What NMR Relaxation Can Tell Us about the Internal Motion of an RNA Hairpin: A Molecular Dynamics Simulation Study

1 reference

12 December 2020

Phenylalanine transfer RNA: molecular dynamics simulation

1 reference

12 December 2020

Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA

1 reference

12 December 2020

Identifiers

DOI

10.1002/BIP.20620

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17080418%20AND%20SRC:MED&resulttype=core&format=json

21 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17080418%20AND%20SRC:MED&resulttype=core&format=json

21 December 2019

PubMed publication ID

17080418

1 reference