Sequence-dependent DNA deformability studied using molecular dynamics simulations (Q42734623)

6 November 2017

Sequence-dependent DNA deformability studied using molecular dynamics simulations (English)

1 reference

6 November 2017

Satoshi Fujii

1 reference

6 November 2017

Hidetoshi Kono

1 reference

6 November 2017

Shigeori Takenaka

1 reference

6 November 2017

Nobuhiro Go

1 reference

6 November 2017

Akinori Sarai

1 reference

6 November 2017

language of work or name

English

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publication date

30 August 2007

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6 November 2017

Nucleic Acids Research

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6 November 2017

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6 November 2017

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6 November 2017

6063-6074

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describes a project that uses

6 November 2017

molecular dynamics simulation

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

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

What drives proteins into the major or minor grooves of DNA?

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

A genomic code for nucleosome positioning

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Protein-DNA recognition patterns and predictions.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Finishing the euchromatic sequence of the human genome

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

DNA and its counterions: a molecular dynamics study

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Structure of the sporulation-specific transcription factor Ndt80 bound to DNA.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

The papillomavirus E2 proteins: structure, function, and biology

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Sequence-dependent DNA structure: tetranucleotide conformational maps

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Structure-based prediction of DNA target sites by regulatory proteins.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Fluctuations of an α‐helix

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Kinking occurs during molecular dynamics simulations of small DNA minicircles

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Sequence-dependent DNA structure: a database of octamer structural parameters

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2094071

Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17766249

12 December 2020

inferred from PubMed ID database lookup

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17766249

12 December 2020

inferred from PubMed ID database lookup

Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17766249

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1093/NAR/GKM627

1 reference

6 November 2017

1 reference

6 November 2017

PubMed publication ID

17766249

1 reference