A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. (Q33566434)

28 July 2017

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

1 reference

nearest neighbour algorithm

28 July 2017

1 reference

inferred from title

author

Thomas E. Cheatham, III

6

Thomas Cheatham

1 reference

28 July 2017

Alberto Perez

15

0 references

Charles Laughton

Charles Laughton

10

0 references

Richard Lavery

Richard Lavery

1

0 references

Jirí Sponer

Jiri Sponer

18

0 references

Modesto Orozco

14

Modesto Orozco

1 reference

28 July 2017

Krystyna Zakrzewska

2

1 reference

28 July 2017

David Beveridge

3

1 reference

28 July 2017

Thomas C Bishop

4

1 reference

28 July 2017

David A Case

5

1 reference

28 July 2017

Surjit Dixit

7

1 reference

28 July 2017

B Jayaram

8

1 reference

28 July 2017

Filip Lankas

9

1 reference

28 July 2017

John H Maddocks

11

1 reference

28 July 2017

Alexis Michon

12

1 reference

28 July 2017

Roman Osman

13

1 reference

28 July 2017

Tanya Singh

16

1 reference

28 July 2017

Nada Spackova

17

1 reference

28 July 2017

language of work or name

English

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publication date

22 October 2009

1 reference

28 July 2017

Nucleic Acids Research

1 reference

28 July 2017

38

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28 July 2017

1

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28 July 2017

299-313

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Conformational analysis of nucleic acids revisited: Curves+

28 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Signatures of Protein-DNA Recognition in Free DNA Binding Sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Recent advances in the study of nucleic acid flexibility by molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Towards a molecular dynamics consensus view of B-DNA flexibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Sequence-dependent DNA deformability studied using molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

A genomic code for nucleosome positioning

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

The Amber biomolecular simulation programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Ion motions in molecular dynamics simulations on DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

DNA and its counterions: a molecular dynamics study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Simulation and modeling of nucleic acid structure, dynamics and interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Measurement of histone-DNA interaction free energy in nucleosomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Residual dipolar couplings in nucleic acid structure determination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Molecular dynamics applied to nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Dipolar couplings in macromolecular structure determination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Helix bending as a factor in protein/DNA recognition.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

How proteins recognize the TATA box

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

"...the tyranny of the lattice...".

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Crystal structure analysis of a complete turn of B-DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Definitions and nomenclature of nucleic acid structure components

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

Dynamics of B-DNA on the microsecond time scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

Importance of accurate DNA structures in solution: the Jun-Fos model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

Sequence-dependent DNA structure: a database of octamer structural parameters.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

The missing term in effective pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

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%2FGKP834

CURVATURE: software for the analysis of curved DNA.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800215

Molecular dynamics with coupling to an external bath

31 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP834

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

21 January 2018

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

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

12 December 2020

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKP834

1 reference

28 July 2017

1 reference

28 July 2017

1 reference