(Q30544923)

English

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

17 October 2017

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations (English)

1 reference

Europe PubMed Central

17 October 2017

molecular dynamics simulation

0 references

1 reference

based on heuristic

inferred from title

Thomas E. Cheatham, III

3

object named as

Thomas E Cheatham

1 reference

Europe PubMed Central

17 October 2017

author name string

Niel M Henriksen

1

1 reference

Europe PubMed Central

17 October 2017

Daniel R Roe

2

1 reference

Europe PubMed Central

17 October 2017

language of work or name

0 references

publication date

4 April 2013

1 reference

Europe PubMed Central

17 October 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

17 October 2017

117

1 reference

Europe PubMed Central

17 October 2017

4014-4027

1 reference

Europe PubMed Central

17 October 2017

15

1 reference

Europe PubMed Central

17 October 2017

Exchange Often and Properly in Replica Exchange Molecular Dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Excited states of ribosome translocation revealed through integrative molecular modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Equilibrium sampling in biomolecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Computational exploration of mobile ion distributions around RNA duplex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Error and efficiency of replica exchange molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

TIGER2: an improved algorithm for temperature intervals with global exchange of replicas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Long-timescale molecular dynamics simulations of protein structure and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Assessing the performance of implicit solvation models at a nucleic acid surface

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Molecular dynamics simulations of nucleic acid-protein complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

UCSF Chimera--a visualization system for exploratory research and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Generalized-ensemble algorithms for molecular simulations of biopolymers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Molecular dynamics simulation of nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

20 June 2018

Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

Folding of a small RNA hairpin based on simulation with replica exchange molecular dynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

How hot? Systematic convergence of the replica exchange method using multiple reservoirs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

A temperature predictor for parallel tempering simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

Atomic simulations of protein folding, using the replica exchange algorithm.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775460

26 November 2018

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Exchange frequency in replica exchange molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RNA stability under different combinations of amber force fields and solvation models

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: insights from molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg

1 reference

https://pubmed.ncbi.nlm.nih.gov/23477537

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP400530E

1 reference

Europe PubMed Central

17 October 2017

1 reference

Europe PubMed Central

17 October 2017

1 reference

Europe PubMed Central

17 October 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q30544923&oldid=1954072850"