(Q30501206)

15 October 2017

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data (English)

1 reference

cryogenic electron microscopy

15 October 2017

0 references

2

Batsal Devkota

0 references

Geoffrey C Rollins

object named as

Geoffrey C Rollins

series ordinal

3

0 references

author name string

Thomas R Caulfield

series ordinal

1

1 reference

PMC publication ID

3116532

15 October 2017

Batsal Devkota

series ordinal

2

1 reference

15 October 2017

28 March 2011

1 reference

15 October 2017

Journal of biophysics

1 reference

15 October 2017

2011

1 reference

15 October 2017

219515

1 reference

Creative Commons Attribution 3.0 Unported

15 October 2017

start time

28 March 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

GTPase activation of elongation factor EF-Tu by the ribosome during decoding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

High performance computing in biology: multimillion atom simulations of nanoscale systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Molecular dynamics simulations of sarcin-ricin rRNA motif.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Simulating movement of tRNA into the ribosome during decoding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

The distribution and query systems of the RCSB Protein Data Bank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Locking and unlocking of ribosomal motions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Visualizing tmRNA entry into a stalled ribosome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Crystal structure of the ribosome at 5.5 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Correlation between three-dimensional structure and chemical reactivity of transfer RNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Analysis of birefringence decay profiles for nucleic acid helices possessing bends: the tau-ratio approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Structure of yeast phenylalanine tRNA at 3 Å resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Detection of a major conformational change in transfer ribonucleic acid by laser light scattering

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116532

Molecular dynamics of phenylalanine transfer RNA.

20 June 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Stochastic gating and drug-ribosome interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Conformational transitions using molecular dynamics with minimum biasing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Intramolecular flexibility in phenylalanine transfer RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1155%2F2011%2F219515

Phenylalanine transfer RNA: molecular dynamics simulation

21 January 2018

1 reference

12 December 2020

The structure of yeast tRNA(Asp). A model for tRNA interacting with messenger RNA

1 reference

12 December 2020

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

1 reference

12 December 2020

Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes

1 reference

12 December 2020

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides 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

Crystal structure of yeast tRNAAsp: atomic coordinates

1 reference

12 December 2020

Identifiers

DOI

10.1155/2011/219515

1 reference

15 October 2017

1 reference

PMC publication ID

3116532

15 October 2017

PubMed publication ID

21716650

1 reference

PMC publication ID

3116532