Analyzing ion distributions around DNA. (Q33843177)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

title

Analyzing ion distributions around DNA (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

John H Maddocks

1 reference

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20 March 2020

Krystyna Zakrzewska

series ordinal

1 reference

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20 March 2020

language of work or name

English

0 references

publication date

6 June 2014

1 reference

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20 March 2020

published in

Nucleic Acids Research

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20 March 2020

volume

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20 March 2020

issue

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20 March 2020

page(s)

8138-8149

1 reference

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Creative Commons Attribution-NonCommercial 3.0 Unported

20 March 2020

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Understanding nucleic acid-ion interactions

1 reference

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

28 July 2018

1 reference

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

28 July 2018

1 reference

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

28 July 2018

1 reference

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Ion and Solvent Density Distributions around Canonical B-DNA from Integral Equations

28 July 2018

1 reference

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

28 July 2018

1 reference

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Conformational analysis of nucleic acids revisited: Curves+

28 July 2018

1 reference

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Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

28 July 2018

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

28 July 2018

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28 July 2018

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The Amber biomolecular simulation programs

28 July 2018

1 reference

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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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

DNA and its counterions: a molecular dynamics study

28 July 2018

1 reference

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

28 July 2018

1 reference

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Locating monovalent cations in the grooves of B-DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

DNA structure: what's in charge?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

DNA structure: cations in charge?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081102

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

28 July 2018

1 reference

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

SAXS studies of ion-nucleic acid interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

Dynamics of B-DNA on the microsecond time scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

The missing term in effective pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

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%2FGKU504

Visualizing density maps with UCSF Chimera

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

Importance of coulombic end effects on cation accumulation near oligoelectrolyte B-DNA: a demonstration using 23Na NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU504

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%2FGKU504

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/24906882

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKU504

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

PubMed publication ID

24906882

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24906882%20AND%20SRC:MED&resulttype=core&format=json