(Q40222512)

18 September 2017

Molecular dynamics simulations of solvated yeast tRNA(Asp). (English)

1 reference

18 September 2017

Auffinger P

1

1 reference

18 September 2017

Louise-May S

series ordinal

2

1 reference

18 September 2017

Westhof E

series ordinal

3

1 reference

18 September 2017

language of work or name

English

0 references

publication date

1 January 1999

1 reference

18 September 2017

1 reference

18 September 2017

76

1 reference

18 September 2017

1 Pt 1

1 reference

18 September 2017

50-64

1 reference

Mg2+ binding and structural stability of mature and in vitro synthesized unmodified Escherichia coli tRNAPhe

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Global flexibility of tertiary structure in RNA: yeast tRNAPhe as a model system

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Compilation of tRNA sequences and sequences of tRNA genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Structure, recognition and adaptive binding in RNA aptamer complexes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Hierarchy and dynamics of RNA folding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Inferring the conformation of RNA base pairs and triples from patterns of sequence variation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

A sampling problem in molecular dynamics simulations of macromolecules

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

The occurrence of C-H...O hydrogen bonds in proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Problems in simulating macromolecular movements

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Crystal structure of an RNA dodecamer containing the Escherichia coli Shine-Dalgarno sequence

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Nuclear magnetic resonance studies on yeast tRNAPhe I. Assignment of the iminoproton resonances of the acceptor and D stem by means of Nuclear Overhauser Effect experiments at 500 MHz

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Nuclear magnetic resonance observation of the triple interaction between A9 and AU12 in yeast tRNAPhe

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Anticodon-anticodon interaction induces conformational changes in tRNA: yeast tRNAAsp, a model for tRNA-mRNA recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Crystallographic structure of an RNA helix: [U(UA)6A]2

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Structural domains of transfer RNA molecules

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Simulations of the molecular dynamics of nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

A crystallographic study of metal-binding to yeast phenylalanine transfer RNA

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Calculations of nucleic acid conformations

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

C-H...O hydrogen bonding in biology

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Transfer RNA(Phe) isoacceptors possess non-identical set of identity elements at high and low Mg2+ concentration.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

NMR studies of ion binding to Escherichia coli tRNAPhe.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Assignment of the low-field 1H NMR spectrum of Escherichia coli tRNAPhe using nuclear Overhauser effects.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Processes of base-pair opening and proton exchange in Z-DNA.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Assignment of the magnetic resonances of the imino protons and methyl protons of Bombyx mori tRNA(GlyGCC) and the effect of ion binding on its structure

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Conformational changes of transfer RNA. The role of magnesium(II)

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Equilibrium binding of magnesium(II) by Escherichia coli tRNAfMet

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Structural elements that contribute to an unusual tertiary interaction in a transfer RNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Nucleoside modifications stabilize Mg2+ binding in Escherichia coli tRNA(Val): an imino proton NMR investigation.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Effect of nucleoside modifications on the structure and thermal stability of Escherichia coli valine tRNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Identification of base-triples in RNA using comparative sequence analysis.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

NMR study of isoleucine transfer RNA from Thermus thermophilus.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302499

Hydration of C-H groups in tRNA

2 December 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Rules governing the orientation of the 2'-hydroxyl group in RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

The missing term in effective pair potentials

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Proton exchange and basepair kinetics of yeast tRNA(Phe) and tRNA(Asp1)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Structure of an unmodified tRNA molecule

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Molecular dynamics investigations of hammerhead ribozyme RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Internal motions of transfer RNA: a study of exchanging protons by magnetic resonance

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Crystal structure of yeast tRNAAsp

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Biostructural chemistry of magnesium ion: characterization of the weak binding sites on tRNA(Phe)(yeast). Implications for conformational change and activity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

Crystallographic refinement of yeast aspartic acid transfer RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

A smooth particle mesh Ewald method

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977177-8

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(99)77177-8

1 reference

18 September 2017

1 reference

18 September 2017

1 reference