(Q29615408)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

title

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

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=17351000

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

0 references

0 references

1

1 reference

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27 December 2019

Daniel Svozil

3

1 reference

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27 December 2019

Jirí Sponer

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

7

Modesto Orozco

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

author name string

Iván Marchán

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

Thomas E Cheatham

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

Charles A Laughton

6

1 reference

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=17351000

27 December 2019

language of work or name

1 reference

30 April 2017

publication date

9 March 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

number of pages

13

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=17351000

inferred from page(s)

2 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

volume

92

2 references

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30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

page(s)

3817-3829

1 reference

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27 December 2019

issue

11

2 references

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30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

Molecular dynamics simulations of sarcin-ricin rRNA motif.

27 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Dynamics of folded proteins

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Nature of minor-groove binders-DNA complexes in the gas phase.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

The relative flexibility of B-DNA and A-RNA duplexes: database analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Ion motions in molecular dynamics simulations on DNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

DNA and its counterions: a molecular dynamics study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Simulation and modeling of nucleic acid structure, dynamics and interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Theoretical methods for the simulation of nucleic acids.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Simulations of nucleic acids and their complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

DNA structure from A to B.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

DNA structure: what's in charge?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Molecular dynamics simulation of nucleic acids

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Nucleic acids: theory and computer simulation, Y2K.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

G-quadruplexes can maintain their structure in the gas phase.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1868997

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

26 November 2018

1 reference

12 December 2020

Role of sugar re-puckering in the transition of A and B forms of DNA in solution. A molecular dynamics study

1 reference

12 December 2020

The Structure and Dynamics of DNA in the Gas Phase

1 reference

12 December 2020

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

12 December 2020

Structure, Recognition Properties, and Flexibility of the DNA·RNA Hybrid

1 reference

12 December 2020

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

1 reference

12 December 2020

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

1 reference

12 December 2020

Principles of RNA Base Pairing: Structures and Energies of the Trans Watson−Crick/Sugar Edge Base Pairs

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

Dynamics of DNA oligomers

1 reference

12 December 2020

Computer simulation of DNA double-helix dynamics

1 reference

12 December 2020

NMR assignments and solution conformation of the DNA.RNA hybrid duplex d(GTGAACTT).r(AAGUUCAC)

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.097782

Identifiers

DOI

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=17351000

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=17351000

3 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17351000%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=17351000

30 April 2017