A coarse-grained model of DNA with explicit solvation by water and ions (Q34481643)

2 August 2017

A coarse-grained model of DNA with explicit solvation by water and ions (English)

1 reference

2 August 2017

Thomas E. Cheatham, III

series ordinal

2

object named as

Thomas E Cheatham

1 reference

2 August 2017

3

Valeria Molinero

1 reference

2 August 2017

Robert C DeMille

1

1 reference

PubMed ID

21155552

2 August 2017

language of work or name

English

0 references

publication date

14 December 2010

1 reference

Journal of Physical Chemistry B

2 August 2017

1 reference

2 August 2017

115

1 reference

2 August 2017

1

1 reference

2 August 2017

132-142

1 reference

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

2 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Using DNA to Link Gold Nanoparticles, Polymers and Molecules: a Theoretical Perspective.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Growing correlation length in supercooled water

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

A mesoscale model of DNA and its renaturation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

A short guide for molecular dynamics simulations of RNA systems.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Insights on protein-DNA recognition by coarse grain modelling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Recent advances in the study of nucleic acid flexibility by molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Molecular dynamics simulations of nucleic acid-protein complexes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Conductimetric determination of thermodynamic pairing constants for symmetrical electrolytes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Simulation and modeling of nucleic acid structure, dynamics and interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Nucleic acids: theory and computer simulation, Y2K.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

From atomic to mesoscopic descriptions of the internal dynamics of DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

The B-DNA dodecamer at high resolution reveals a spine of water on sodium

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Particle-Based Implicit Solvent Model for Biosimulations: Application to Proteins and Nucleic Acids Hydration.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Amorphous precursors in the nucleation of clathrate hydrates.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Ice crystallization in water's "no-man's land".

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

DNA melting in small-molecule-DNA-hybrid dimer structures: experimental characterization and coarse-grained molecular dynamics simulations

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Water modeled as an intermediate element between carbon and silicon

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

A coarse grain model for DNA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Theory of counter-ion condensation on flexible polyelectrolytes: adsorption mechanism.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

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.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Supercoiling and Local Denaturation of Plasmids with a Minimalist DNA Model

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3019136

Counterion association with native and denatured nucleic acids: an experimental approach

9 December 2018

1 reference

12 December 2020

A methane-water model for coarse-grained simulations of solutions and clathrate hydrates.

1 reference

12 December 2020

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

1 reference

12 December 2020

Thermodynamic stability and growth of guest-free clathrate hydrates: a low-density crystal phase of water

1 reference

12 December 2020

Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution

1 reference

12 December 2020

Amorphous silica modeled with truncated and screened Coulomb interactions: a molecular dynamics simulation study

1 reference

12 December 2020

A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties

1 reference

12 December 2020

Modeling DNA deformations

1 reference

12 December 2020

Computer simulation of local order in condensed phases of silicon

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP107028N

1 reference

2 August 2017

1 reference

2 August 2017

1 reference

PubMed ID

21155552