(Q26799988)

2

0 references

Jessica D Leuchter

3

0 references

Rebecca W Alexander

4

0 references

Samuel S Cho

International Journal of Molecular Sciences

5

0 references

language of work or name

English

0 references

publication date

2015

0 references

13 July 2015

1 reference

19 September 2019

2 references

19 September 2019

28 September 2019

16

0 references

issue

7

0 references

page(s)

15872-902

0 references

copyright license

Creative Commons Attribution

2 references

19 September 2019

28 September 2019

0 references

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

CHARMM: the biomolecular simulation program

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Two distinct cytokines released from a human aminoacyl-tRNA synthetase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The Structure of Yeast Glutaminyl-tRNA Synthetase and Modeling of Its Interaction with tRNA

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Peripheral insertion modulates the editing activity of the isolated CP1 domain of leucyl-tRNA synthetase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

All-atom empirical potential for molecular modeling and dynamics studies of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Scalable molecular dynamics with NAMD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The Amber biomolecular simulation programs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Effective Born radii in the generalized Born approximation: the importance of being perfect

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Exposing the kinetic traps in RNA folding

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

7 April 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Principles that govern the folding of protein chains

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Development and testing of a general amber force field

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Non-coding RNAs in human disease

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

7 April 2017

Aminoacyl-tRNA synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Recent development and application of constant pH molecular dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Modulation of frustration in folding by sequence permutation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The significance of the 2013 Nobel Prize in Chemistry and the challenges ahead

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Synthetic and editing mechanisms of aminoacyl-tRNA synthetases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Structural diversity and protein engineering of the aminoacyl-tRNA synthetases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Kinetic partitioning between synthetic and editing pathways in class I aminoacyl-tRNA synthetases occurs at both pre-transfer and post-transfer hydrolytic steps

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Biomolecular simulation: a computational microscope for molecular biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Role of coupled dynamics in the catalytic activity of prokaryotic-like prolyl-tRNA synthetases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Kinetics of tRNA folding monitored by aminoacylation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Fast folding of RNA pseudoknots initiated by laser temperature-jump

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Exit strategies for charged tRNA from GluRS

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The balance between pre- and post-transfer editing in tRNA synthetases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Insights from coarse-grained Gō models for protein folding and dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Dynamical networks in tRNA:protein complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Dynamics of tRNA at different levels of hydration.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Minimal models for proteins and RNA from folding to function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Coevolution of function and the folding landscape: correlation with density of native contacts

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Aminoacyl tRNA synthetases and their connections to disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Extracting function from a beta-trefoil folding motif

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Accelerating molecular modeling applications with graphics processors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Mechanism of the difference in the binding affinity of E. coli tRNAGln to glutaminyl-tRNA synthetase caused by noninterface nucleotides in variable loop

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Mechanical unfolding of RNA hairpins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Escaping free-energy minima

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The origins of asymmetry in the folding transition states of protein L and protein G.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The chemical repertoire of natural ribozymes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

An expanding universe of noncoding RNAs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Domain-domain communication in aminoacyl-tRNA synthetases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Induced fit in RNA-protein recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Fast kinetics and mechanisms in protein folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

RNA folding causes secondary structure rearrangement

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Simulations of the molecular dynamics of nucleic acids

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Transition state stabilization by the 'high' motif of class I aminoacyl-tRNA synthetases: the case of Escherichia coli methionyl-tRNA synthetase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Navigating the folding routes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Structure of yeast phenylalanine tRNA at 3 Å resolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Flexibility and Rigidity in Protein Crystals

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Structural states of the flexible catalytic loop of M. tuberculosis tyrosyl-tRNA synthetase in different enzyme-substrate complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Identification of the tRNA anticodon recognition site of Escherichia coli methionyl-tRNA synthetase.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

The crystal structure of tyrosyl-transfer RNA synthetase at 2-7 A resolution

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Conformational changes of transfer ribonucleic acid. Comparison of the early melting transition of two tyrosine-specific transfer ribonucleic acids.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Aminoacylation of tRNAs as critical step of protein biosynthesis

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Eppur si muove! The 2013 Nobel Prize in Chemistry

31 May 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Refinement of the application of the GROMOS 54A7 force field to β-peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Topology links RNA secondary structure with global conformation, dynamics, and adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Mg2+-induced tRNA folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Does native state topology determine the RNA folding mechanism?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Topological frustration and the folding of interleukin-1 beta

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Identification of the nucleophilic factors and the productive complex for the editing reaction by leucyl-tRNA synthetase

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Molecular dynamics simulation study of valyl-tRNA synthetase with its pre- and post-transfer editing substrates.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Molecular Dynamics Simulations Show That Bound Mg2+Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Template-based structure prediction and molecular dynamics simulation study of two mammalian Aspartyl-tRNA synthetases.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Molecular dynamics simulations of LysRS: an asymmetric state.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Structural basis for anticodon recognition by methionyl-tRNA synthetase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Shape-selective RNA recognition by cysteinyl-tRNA synthetase

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

Substrate-assisted catalysis in the aminoacyl transfer mechanism of histidyl-tRNA synthetase: a density functional theory study

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

21 January 2018

2 references

https://api.crossref.org/works/10.3390%2FIJMS160715872

21 January 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4519929

Pseudomonic acid, a new antibiotic for topical therapy

28 November 2018

1 reference

12 December 2020

CHARMM-GUI: a web-based graphical user interface for CHARMM

1 reference

12 December 2020

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

Asymmetric structure and domain binding interfaces of human tyrosyl-tRNA synthetase studied by molecular dynamics simulations

1 reference

12 December 2020

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

1 reference

12 December 2020

Interdomain compactization in human tyrosyl-tRNA synthetase studied by the hierarchical rotations technique

1 reference

12 December 2020

Computational studies of tryptophanyl-tRNA synthetase: activation of ATP by induced-fit

1 reference

12 December 2020

Molecular dynamics investigation into substrate binding and identity of the catalytic base in the mechanism of Threonyl-tRNA synthetase

1 reference

12 December 2020

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

1 reference

12 December 2020

High resolution NMR study of the melting of tRNAYeastPhe

1 reference

12 December 2020

Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams

1 reference

12 December 2020

Enzymatic carboxyl activation of amino acids

1 reference

12 December 2020

Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments

1 reference

12 December 2020

Molecular trigger for pre-transfer editing pathway in Valyl-tRNA synthetase: a molecular dynamics simulation study

1 reference

12 December 2020

Self-strengthening biphasic nanoparticle assemblies with intrinsic catch bonds

1 reference

https://api.crossref.org/works/10.3390%2FIJMS160715872

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.3390/IJMS160715872

1 reference

1 reference

1 reference

PubMed publication ID

26184179

1 reference