(Q37621655)

21 August 2017

Ion counting from explicit-solvent simulations and 3D-RISM. (English)

1 reference

21 August 2017

4

Darrin M York

1 reference

21 August 2017

George M Giambaşu

1

1 reference

21 August 2017

Tyler Luchko

series ordinal

2

1 reference

21 August 2017

Daniel Herschlag

series ordinal

3

1 reference

21 August 2017

David A Case

series ordinal

5

1 reference

21 August 2017

language of work or name

English

0 references

publication date

1 February 2014

1 reference

21 August 2017

1 reference

21 August 2017

106

1 reference

21 August 2017

4

1 reference

21 August 2017

883-894

1 reference

The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

RNA and its ionic cloud: solution scattering experiments and atomically detailed 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=3944826

SAXS studies of ion-nucleic acid interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Solvent and salt effects on structural stability of human telomere

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Ion and solvent density distributions around canonical B-DNA from integral equations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Computational exploration of mobile ion distributions around RNA duplex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift 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=3944826

RNA folding: thermodynamic and molecular descriptions of the roles of ions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary 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=3944826

Relative binding affinities of monovalent cations for double-stranded 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=3944826

Equilibrium dialysis data and the relationships between preferential interaction parameters for biological systems in terms of Kirkwood-Buff integrals

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Scalable molecular dynamics with NAMD

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

The Amber biomolecular simulation programs

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Ion motions in molecular dynamics simulations on 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=3944826

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and 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=3944826

Electrostatics of nanosystems: application to microtubules and the ribosome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

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=3944826

Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Quantitative and comprehensive decomposition of the ion atmosphere around 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=3944826

Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Water and ion binding around RNA and DNA (C,G) 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=3944826

Salt-nucleic acid interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

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=3944826

Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Efficient treatment of solvation shells in 3D molecular theory of solvation.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Counting ions around DNA with anomalous small-angle X-ray scattering.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

DNA attraction in monovalent and divalent electrolytes

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

A protein molecule in a mixed solvent: the preferential binding parameter via the Kirkwood-Buff theory

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

A counterion condensation theory for the relaxation, rise, and frequency dependence of the parallel polarization of rodlike polyelectrolytes.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Probing Nucleic Acid–Ion Interactions with Buffer Exchange-Atomic Emission Spectroscopy

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Counterion Condensation on Charged Spheres, Cylinders, and Planes†

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3944826

Simulations of RNA Interactions with Monovalent Ions

3 December 2018

1 reference

12 December 2020

Revisiting the salt-induced conformational change of DNA with 3D-RISM theory

1 reference

12 December 2020

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point

1 reference

12 December 2020

The impact of monovalent ion force field model in nucleic acids simulations

1 reference

12 December 2020

Optimised parameters for A-DNA and B-DNA

1 reference

12 December 2020

Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules

1 reference

12 December 2020

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

1 reference

12 December 2020

Competitive interactions of Co(NH3)6(3+) and Na+ with helical B-DNA probed by 59Co and 23Na NMR

1 reference

12 December 2020

10.1016/J.BPJ.2014.01.021

Identifiers

DOI

1 reference

21 August 2017

1 reference

21 August 2017

PubMed publication ID

24559991

1 reference