(Q34188047)

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

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15326025%20AND%20SRC:MED&resulttype=core&format=json

31 December 2019

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

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31 December 2019

molecular design

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31 December 2019

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31 December 2019

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31 December 2019

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David L Beveridge

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31 December 2019

Gabriela Barreiro

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31 December 2019

K Suzie Byun

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31 December 2019

David A Case

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31 December 2019

Surjit B Dixit

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31 December 2019

Emmanuel Giudice

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31 December 2019

Filip Lankas

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31 December 2019

John H Maddocks

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31 December 2019

Roman Osman

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31 December 2019

Eleanore Seibert

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31 December 2019

Heinz Sklenar

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31 December 2019

Kelly M Thayer

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31 December 2019

Péter Varnai

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31 December 2019

Thomas E Cheatham

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31 December 2019

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23 August 2004

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31 December 2019

Biophysical Journal

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31 December 2019

87

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31 December 2019

6

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31 December 2019

3799-3813

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31 December 2019

describes a project that uses

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26 June 2022

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Ion motions in molecular dynamics simulations on DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

DNA and its counterions: a molecular dynamics study

1 reference

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5 July 2018

Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting

1 reference

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5 July 2018

Theoretical methods for the simulation of nucleic acids.

1 reference

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5 July 2018

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

DNA polymorphism: a comparison of force fields for nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Structural origins of adenine-tract bending

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Alpha/gamma transitions in the B-DNA backbone

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Residual dipolar couplings in nucleic acid structure determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Molecular dynamics applied to nucleic acids

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Simulations of nucleic acids and their complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Development and current status of the CHARMM force field for nucleic acids.

1 reference

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5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Molecular dynamics simulation of nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Nucleic acids: theory and computer simulation, Y2K.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Sequence-dependent DNA structure: tetranucleotide conformational maps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Overview of nucleic acid analysis programs

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Resolving the discrepancies among nucleic acid conformational analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Helix bending as a factor in protein/DNA recognition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

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5 July 2018

Structural equilibrium of DNA represented with different force fields

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304892

5 July 2018

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

1 reference

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5 July 2018

Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA.

1 reference

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5 July 2018

Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

1 reference

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5 July 2018

BI-BII transitions in B-DNA.

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5 July 2018

Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides

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5 July 2018

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

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5 July 2018

Crystal structure analysis of a complete turn of B-DNA

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5 July 2018

Structure of a B-DNA dodecamer: conformation and dynamics

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5 July 2018

Sequence periodicities in chicken nucleosome core DNA.

1 reference

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5 July 2018

Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract

1 reference

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5 July 2018

The conformation of the DNA double helix in the crystal is dependent on its environment

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5 July 2018

The effect of crystal packing on oligonucleotide double helix structure

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5 July 2018

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

1 reference

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5 July 2018

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers

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5 July 2018

Conformational sub-states in B-DNA.

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5 July 2018

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

1 reference

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28 October 2018

Dynamics and structures of DNA: long-range effects of a 16 base-pair (CG)8 sequence on secondary structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

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1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants

1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure of a B-DNA dodecamer. III. Geometry of hydration

1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The unusual conformation adopted by the adenine tracts in kinetoplast DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/15326025

12 December 2020

based on heuristic

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Identifiers

10.1529/BIOPHYSJ.104.045252

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31 December 2019

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31 December 2019

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31 December 2019

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