(Q35131148)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

title

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

Richard Lavery

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

author name string

John H Maddocks

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

language of work or name

English

0 references

publication date

6 February 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

number of pages

12

1 reference

based on heuristic

inferred from page(s)

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

volume

43

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

page(s)

2412-2423

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 4.0 International

29 February 2020

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Analyzing ion distributions around DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Understanding nucleic acid-ion interactions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Exploring polymorphisms in B-DNA helical conformations.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Frontiers in molecular dynamics simulations of DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

SAXS studies of ion-nucleic acid interactions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Conformational analysis of nucleic acids revisited: Curves+

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Nucleic acid solvation: from outside to insight.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

The DNA structure responds differently to physiological concentrations of K(+) or Na(+).

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Visualizing density maps with UCSF Chimera

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

The Amber biomolecular simulation programs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Ion motions in molecular dynamics simulations on DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

DNA and its counterions: a molecular dynamics study

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

UCSF Chimera--a visualization system for exploratory research and analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Competitive Na(+) and Rb(+) binding in the minor groove of DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Locating monovalent cations in the grooves of B-DNA

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

DNA structure: what's in charge?

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Sequence-specific binding of counterions to B-DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Sodium and chlorine ions as part of the DNA solvation shell

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

DNA structure: cations in charge?

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

The molecular origin of DNA-drug specificity in netropsin and distamycin

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

The electrostatic potential of B-DNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Water: an integral part of nucleic acid structure

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

Dynamics of B-DNA on the microsecond time scale.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344516

The missing term in effective pair potentials

27 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

Matplotlib: A 2D Graphics Environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

The Dickerson-Drew B-DNA Dodecamer Revisited at Atomic Resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV080

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25662221

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Nonspecific DNA-protein interaction: why proteins can diffuse along DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25662221

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKV080

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25662221%20AND%20SRC:MED&resulttype=core&format=json