(Q41299060)

29 September 2017

Local and global effects of strong DNA bending induced during molecular dynamics simulations (English)

1 reference

29 September 2017

2

Martin Zacharias

1 reference

29 September 2017

Jeremy Curuksu

1

1 reference

29 September 2017

Richard Lavery

series ordinal

3

1 reference

29 September 2017

Krystyna Zakrzewska

series ordinal

4

1 reference

29 September 2017

20 April 2009

1 reference

29 September 2017

Nucleic Acids Research

1 reference

29 September 2017

37

1 reference

29 September 2017

11

1 reference

29 September 2017

3766-3773

1 reference

Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA stretching and extreme kinking in the nucleosome core

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Spontaneous sharp bending of DNA: role of melting bubbles

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Minor groove deformability of DNA: a molecular dynamics free energy simulation study

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Generalized theory of semiflexible polymers

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Biocompatible force sensor with optical readout and dimensions of 6 nm3.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA dynamics: bubble 'n' flip for DNA cyclisation?

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Exact theory of kinkable elastic polymers.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Structure and axis curvature in two dA6 x dT6 DNA oligonucleotides: comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Stacked-unstacked equilibrium at the nick site of DNA

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA and its counterions: a molecular dynamics study

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA sequence-dependent deformability--insights from computer simulations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Role of DNA sequence in nucleosome stability and dynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Crystal structure of the nucleosome core particle at 2.8 A resolution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

The locus of sequence-directed and protein-induced DNA bending

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Sequence-dependent bending of DNA and phasing of nucleosomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Defining the structure of irregular nucleic acids: conventions and principles

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Determination of the extent of DNA bending by an adenine-thymine tract

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Organization of DNA in chromatin

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Anisotropic flexibility of DNA and the nucleosomal structure

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Sequence-dependent DNA structure: tetranucleotide conformational maps

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Helix bending as a factor in protein/DNA recognition.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

High flexibility of DNA on short length scales probed by atomic force microscopy.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Kinking occurs during molecular dynamics simulations of small DNA minicircles.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Spontaneous sharp bending of double-stranded DNA.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Analyzing protein-DNA recognition mechanisms.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

DNA deformation energetics and protein binding

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699519

Sequence-Dependent Variability of B-DNA

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKP234

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKP234

B-DNA twisting correlates with base-pair morphology.

21 January 2018

1 reference

12 December 2020

DNA bending and sequence-dependent backbone conformation NMR and computer experiments

1 reference

12 December 2020

DNA bending stiffness on small length scales

1 reference

12 December 2020

Localized single-stranded bubble mechanism for cyclization of short double helix DNA

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKP234

1 reference

29 September 2017

1 reference

29 September 2017

PubMed publication ID

19380377

1 reference