Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. (Q34181373)

31 July 2017

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

1 reference

31 July 2017

5

Jaroslav Koca

1 reference

31 July 2017

Kamila Réblová

1

1 reference

31 July 2017

Nad'a Spacková

2

1 reference

31 July 2017

Richard Stefl

3

1 reference

31 July 2017

Kristina Csaszar

4

1 reference

31 July 2017

Neocles B Leontis

6

1 reference

31 July 2017

Jirí Sponer

7

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 June 2003

1 reference

31 July 2017

19

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

31 July 2017

84

1 reference

31 July 2017

3564-3582

1 reference

31 July 2017

6

1 reference

Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Crystal structure of the potassium form of an Oxytricha nova G-quadruplex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

The free energy landscape for beta hairpin folding in explicit water

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

High resolution structure of the large ribosomal subunit from a mesophilic eubacterium

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Geometric nomenclature and classification of RNA base pairs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Atomic structures at last: the ribosome in 2000.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

DNA structure: what's in charge?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Molecular dynamics of the anticodon domain of yeast tRNA(Phe): codon-anticodon interaction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Molecular dynamics simulation of nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Structure of the 30S ribosomal subunit

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

A-form conformational motifs in ligand-bound DNA structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Archaeal ribosomal protein L1: the structure provides new insights into RNA binding of the L1 protein family

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Nucleic acids: theory and computer simulation, Y2K.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Conserved geometrical base-pairing patterns in RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Stitching together RNA tertiary architectures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Sodium and chlorine ions as part of the DNA solvation shell

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Crystal structure of the ribosomal RNA domain essential for binding elongation factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C.A+ mismatches

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Structure of an RNA internal loop consisting of tandem C-A+ base pairs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Simulations of the molecular dynamics of nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

VMD: visual molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

The conformation of loop E of eukaryotic 5S ribosomal RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

The sarcin/ricin loop, a modular RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

The site of action of alpha-sarcin on eukaryotic ribosomes. The sequence at the alpha-sarcin cleavage site in 28 S ribosomal ribonucleic acid.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Conformational heterogeneity observed in simulations of a pyrene-substituted DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Zipper-like Watson-Crick base-pairs

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Adenine protonation in domain B of the hairpin ribozyme

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302943

RNA solvation: a molecular dynamics simulation perspective

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

A molecular simulation picture of DNA hydration around A- and B-DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

Molecular dynamics investigations of hammerhead ribozyme RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

Wild-Type RNA MicrohelixAlaand 3:70 Variants: Molecular Dynamics Analysis of Local Helical Structure and Tightly Bound Water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

Higher order structure of chloroplastic 5S ribosomal RNA from spinach

7 January 2021

1 reference

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A molecular dynamics simulation study of coaxial stacking in RNA

7 January 2021

1 reference

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Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules

7 January 2021

1 reference

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Nanosecond Molecular Dynamics of Zipper-like DNA Duplex Structures Containing Sheared G·A Mismatch Pairs

7 January 2021

1 reference

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Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

7 January 2021

Nonplanar DNA Base Pairs

1 reference

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Cation—π and Amino-Acceptor Interactions Between Hydrated Metal Cations and DNA Bases. A Quantum-Chemical View

7 January 2021

1 reference

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The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing

7 January 2021

1 reference

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Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals

7 January 2021

1 reference

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Simulation of the structure and dynamics of nonhelical RNA motifs

7 January 2021

1 reference

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A smooth particle mesh Ewald method

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2975089-9

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(03)75089-9

1 reference

31 July 2017

1 reference

31 July 2017

1 reference