The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA (Q24811864)

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English	The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA	scientific article

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scholarly article

1 reference

Europe PubMed Central

5 July 2017

The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA (English)

1 reference

Europe PubMed Central

5 July 2017

potential energy

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object named as

Karim M Elsawy

1

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author name string

Michael K Hodgson

2

1 reference

Europe PubMed Central

5 July 2017

Leo S D Caves

3

1 reference

Europe PubMed Central

5 July 2017

language of work or name

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publication date

7 October 2005

1 reference

Europe PubMed Central

5 July 2017

Nucleic Acids Research

1 reference

Europe PubMed Central

5 July 2017

33

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Europe PubMed Central

5 July 2017

18

1 reference

Europe PubMed Central

5 July 2017

5749-5762

1 reference

Europe PubMed Central

5 July 2017

Structure of a B-DNA dodecamer: conformation and dynamics

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

7 April 2017

Co-crystal structure of TBP recognizing the minor groove of a TATA element

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

7 April 2017

Crystal structure of a yeast TBP/TATA-box complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

7 April 2017

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

7 April 2017

Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G

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7 April 2017

The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

7 April 2017

Stereochemistry of polypeptide chain configurations

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

7 April 2017

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

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7 April 2017

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://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Dynamics of the B-A transition of DNA double helices

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

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=1253833

28 September 2017

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=1253833

28 September 2017

Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Investigating protein dynamics in collective coordinate space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

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=1253833

28 September 2017

Interdependence of conformational variables in double-helical DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

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=1253833

28 September 2017

Theory of electrostatic interactions in macromolecules.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

The effect of the base sequence on the fine structure of the DNA double helix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Helix geometry, hydration, and G.A mismatch in a B-DNA decamer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Sequence-dependent variations in the 31P NMR spectra and backbone torsional angles of wild-type and mutant Lac operator fragments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

The effect of crystal packing on oligonucleotide double helix structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Binding of small acid-soluble spore proteins from Bacillus subtilis changes the conformation of DNA from B to A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 September 2017

Conformations and structural transitions in polydeoxynucleotides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

30 May 2018

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 November 2018

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 November 2018

How NF-κB can be attracted by its cognate DNA

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1253833

28 November 2018

Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

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28 November 2018

B----A transitions within a 5 S ribosomal RNA gene are highly sequence-specific

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleic acid model building: the multiple backbone solutions associated with a given base morphology

1 reference

https://pubmed.ncbi.nlm.nih.gov/16214808

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G

1 reference

https://pubmed.ncbi.nlm.nih.gov/16214808

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/16214808

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/16214808

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

https://pubmed.ncbi.nlm.nih.gov/16214808

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

[Atom--atomic potential functions for conformational calculations of nucleic acids]

1 reference

https://pubmed.ncbi.nlm.nih.gov/16214808

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKI888

1 reference

Europe PubMed Central

5 July 2017

1 reference

Europe PubMed Central

5 July 2017

1 reference

Europe PubMed Central

5 July 2017

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