(Q34410781)

2 August 2017

title

X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation (English)

1 reference

2 August 2017

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Xiaobing Zuo

1

1 reference

2 August 2017

Guanglei Cui

2

1 reference

2 August 2017

Kenneth M Merz

3

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2 August 2017

Ligang Zhang

4

1 reference

2 August 2017

Frederick D Lewis

5

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2 August 2017

David M Tiede

6

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2 August 2017

language of work or name

English

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publication date

27 February 2006

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Proceedings of the National Academy of Sciences of the United States of America

2 August 2017

published in

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2 August 2017

volume

103

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2 August 2017

issue

10

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2 August 2017

page(s)

3534-3539

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The Amber biomolecular simulation programs

2 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

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

6 July 2018

1 reference

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Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

Ion motions in molecular dynamics simulations on DNA.

6 July 2018

1 reference

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Simulation and modeling of nucleic acid structure, dynamics and interactions

6 July 2018

1 reference

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

DNA sequence-dependent deformability--insights from computer simulations

6 July 2018

1 reference

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3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

6 July 2018

1 reference

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Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C.

6 July 2018

1 reference

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Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

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

6 July 2018

1 reference

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Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions

6 July 2018

1 reference

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The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

Statistical analysis of DNA duplex structural features

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

Structure of the alpha-form of poly[d(A)].poly[d(T)] and related polynucleotide duplexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1383498

Structure of an alternating-B DNA helix and its relationship to A-tract DNA

6 July 2018

1 reference

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Charge migration in DNA: ion-gated transport

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrity

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

Structural characterization of modular supramolecular architectures in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

The discovery of the DNA double helix.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

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/10.1073%2FPNAS.0600022103

Conformational heterogeneity observed in simulations of a pyrene-substituted DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0600022103

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

21 January 2018

1 reference

12 December 2020

Structural hierarchy of several proteins observed by wide-angle solution scattering

1 reference

12 December 2020

Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction

1 reference

12 December 2020

B-DNA twisting correlates with base-pair morphology.

1 reference

12 December 2020

Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0600022103

1 reference

2 August 2017

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2 August 2017

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