(Q34352331)

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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

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Europe PubMed Central

PubMed publication ID

1 August 2017

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 (English)

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Europe PubMed Central

PubMed publication ID

1 August 2017

Thomas E. Cheatham, III

4

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Thomas E Cheatham

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1 August 2017

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Surjit B Dixit

1

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1 August 2017

David L Beveridge

2

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1 August 2017

David A Case

3

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1 August 2017

Emmanuel Giudice

5

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1 August 2017

Filip Lankas

6

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1 August 2017

Richard Lavery

7

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1 August 2017

John H Maddocks

8

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1 August 2017

Roman Osman

9

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1 August 2017

Heinz Sklenar

10

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1 August 2017

Kelly M Thayer

11

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1 August 2017

Péter Varnai

12

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1 August 2017

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publication date

16 September 2005

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1 August 2017

number of pages

20

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Biophysical Journal

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1 August 2017

89

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1 August 2017

6

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Europe PubMed Central

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1 August 2017

3721-3740

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Europe PubMed Central

PubMed publication ID

1 August 2017

How sequence defines structure: a crystallographic map of DNA structure and conformation.

1 reference

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6 July 2018

Improving implicit solvent simulations: a Poisson-centric view

1 reference

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6 July 2018

Structure and axis curvature in two dA6 x dT6 DNA oligonucleotides: comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 July 2018

Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method

1 reference

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6 July 2018

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=1366942

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 July 2018

DNA and its counterions: a molecular dynamics study

1 reference

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6 July 2018

Empirical force fields for biological macromolecules: overview and issues.

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6 July 2018

Simulation and modeling of nucleic acid structure, dynamics and interactions

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6 July 2018

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

1 reference

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6 July 2018

Theoretical methods for the simulation of nucleic acids.

1 reference

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6 July 2018

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

1 reference

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6 July 2018

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

1 reference

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6 July 2018

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

1 reference

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6 July 2018

Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 July 2018

A unified model for the origin of DNA sequence-directed curvature.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 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=1366942

6 July 2018

Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 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=1366942

6 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=1366942

6 July 2018

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 July 2018

Molecular dynamics applied to nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 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=1366942

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 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=1366942

6 July 2018

A standard reference frame for the description of nucleic acid base-pair geometry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 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=1366942

6 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=1366942

6 July 2018

The structure of a stable intermediate in the A left-right-arrow B DNA helix transition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

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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=1366942

6 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=1366942

6 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=1366942

6 July 2018

Resolving the discrepancies among nucleic acid conformational analyses

1 reference

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6 July 2018

Helix bending as a factor in protein/DNA recognition.

1 reference

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6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

6 July 2018

BI-BII transitions in B-DNA.

1 reference

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6 July 2018

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

1 reference

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Three-state models of furanose pseudorotation

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1 reference

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6 July 2018

The electrostatic potential of B-DNA.

1 reference

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6 July 2018

Defining the structure of irregular nucleic acids: conventions and principles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

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

1 reference

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6 July 2018

Conformational sub-states in B-DNA.

1 reference

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6 July 2018

Solution structure of a DNA octamer containing the Pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fitting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1366942

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1 reference

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1 reference

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27 October 2018

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

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Sequence-dependent DNA structure: dinucleotide conformational maps

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12 December 2020

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1 reference

https://pubmed.ncbi.nlm.nih.gov/16169978

12 December 2020

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The Nucleic Acid Database

1 reference

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12 December 2020

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1 reference

https://pubmed.ncbi.nlm.nih.gov/16169978

12 December 2020

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12 December 2020

based on heuristic

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1 reference

https://pubmed.ncbi.nlm.nih.gov/16169978

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/16169978

12 December 2020

based on heuristic

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Mechanics of sequence-dependent stacking of bases in B-DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/16169978

12 December 2020

based on heuristic

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Identifiers

10.1529/BIOPHYSJ.105.067397

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

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