Ion motions in molecular dynamics simulations on DNA. (Q37571782)

21 August 2017

Ion motions in molecular dynamics simulations on DNA. (English)

1 reference

21 August 2017

Sergei Y Ponomarev

1

1 reference

21 August 2017

Kelly M Thayer

series ordinal

2

1 reference

21 August 2017

David L Beveridge

series ordinal

3

1 reference

21 August 2017

language of work or name

English

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publication date

1 October 2004

1 reference

Proceedings of the National Academy of Sciences of the United States of America

21 August 2017

1 reference

21 August 2017

101

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21 August 2017

41

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21 August 2017

14771-14775

1 reference

Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Theoretical methods for the simulation of nucleic acids.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Development and current status of the CHARMM force field for nucleic acids.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Locating monovalent cations in the grooves of B-DNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA-cation interactions: The major and minor grooves are flexible ionophores.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Molecular dynamics simulation of nucleic acids

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Electrostatic mechanisms of DNA deformation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Nucleic acids: theory and computer simulation, Y2K.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Sequence-specific binding of counterions to B-DNA.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Sodium and chlorine ions as part of the DNA solvation shell

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA structure: cations in charge?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA Bending by Small, Mobile Multivalent Cations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

The B-DNA Dodecamer at High Resolution Reveals a Spine of Water on Sodium,

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Classical electrostatics in biology and chemistry

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Structure of a B-DNA dodecamer: conformation and dynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Defining the structure of irregular nucleic acids: conventions and principles

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

A unified model for the origin of DNA sequence-directed curvature.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Molecular dynamics simulations of A. T-rich oligomers: sequence-specific binding of Na in the minor groove of B-DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Preferential counterion binding to A-tract DNA oligomers

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA structure: what's in charge?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Effect of base composition on DNA bending by phosphate neutralization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA bending by asymmetric phosphate neutralization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

DNA and its counterions: a molecular dynamics study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG)

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Nucleic acid conformation: crystal structure of a naturally occurring dinucleoside phosphate (UpA).

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

The electrostatic potential of B-DNA.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522050

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

1 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073/PNAS.0406435101

Water and Ions in a High Resolution Structure of B-DNA

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073/PNAS.0406435101

Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation

21 January 2018

1 reference

12 December 2020

Divalent cations stabilize unstacked conformations of DNA and RNA by interacting with base pi systems

1 reference

12 December 2020

Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects

1 reference

12 December 2020

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

12 December 2020

Structure of a B-DNA dodecamer. III. Geometry of hydration

1 reference

12 December 2020

The unusual conformation adopted by the adenine tracts in kinetoplast DNA

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0406435101

1 reference

21 August 2017

0 references

1 reference

21 August 2017

PubMed publication ID

15465909

1 reference