Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics. (Q35866373)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

title

Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Nicolas Foloppe

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Akli Ben Imeddourene

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Christophe Oguey

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Brigitte Hartmann

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

publication date

10 December 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

2 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

page(s)

e1004631

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

2 March 2020

start time

10 December 2015

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

All-atom polarizable force field for DNA based on the classical Drude oscillator model

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

The mechanics behind DNA sequence-dependent properties of the nucleosome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Frontiers in Molecular Dynamics Simulations of DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Structure of RCC1 chromatin factor bound to the nucleosome core particle

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Structural insight into the sequence dependence of nucleosome positioning

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Intrinsic flexibility of B-DNA: the experimental TRX scale

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Towards a molecular dynamics consensus view of B-DNA flexibility

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

The DNA structure responds differently to physiological concentrations of K(+) or Na(+).

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

DNA stretching and extreme kinking in the nucleosome core

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Scalable molecular dynamics with NAMD

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

DNA and its counterions: a molecular dynamics study

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Empirical force fields for biological macromolecules: overview and issues.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

The role of DNA structure and dynamics in the recognition of bovine papillomavirus E2 protein target sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Alpha/gamma transitions in the B-DNA backbone

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form of DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Crystal studies of B-DNA: the answers and the questions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

BI-BII transitions in B-DNA.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

31P NMR spectra of oligodeoxyribonucleotide duplex lac operator-repressor headpiece complexes: importance of phosphate ester backbone flexibility in protein-DNA recognition

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Making the bend: DNA tertiary structure and protein-DNA interactions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Simulating DNA by molecular dynamics: aims, methods, and validation

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Phosphorus chemical shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Sequence-dependent DNA flexibility mediates DNase I cleavage

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

31P NMR investigation of backbone dynamics in DNA binding sites

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Importance of accurate DNA structures in solution: the Jun-Fos model

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

DNA deformation energetics and protein binding

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4689557

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

24 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004631

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004631

How NF-κB can be attracted by its cognate DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004631

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004631

Calibrating nucleic acids torsional energetics in force-field: insights from model compounds

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004631

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

21 January 2018

1 reference

12 December 2020

Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion

1 reference

12 December 2020

NMR studies of DNA support the role of pre-existing minor groove variations in nucleosome indirect readout

1 reference

12 December 2020

Structural behavior of the CpG step in two related oligonucleotides reflects its malleability in solution

1 reference

12 December 2020

Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition

1 reference

12 December 2020

Nucleic acid model building: the multiple backbone solutions associated with a given base morphology

1 reference

12 December 2020

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1004631

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/ImeddoureneEGOF15

2 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

PubMed publication ID

26657165

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26657165%20AND%20SRC:MED&resulttype=core&format=json