(Q34183456)

31 July 2017

DNA basepair step deformability inferred from molecular dynamics simulations (English)

1 reference

31 July 2017

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations (English)

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(03)74710-9

25 March 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

25 March 2024

molecular model

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

25 March 2024

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(03)74710-9

25 March 2024

author

Thomas E. Cheatham, III

4

object named as

Thomas E Cheatham

1 reference

31 July 2017

2

Jirí Sponer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

25 March 2024

3

Jörg Langowski

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

25 March 2024

author name string

Filip Lankas

1

1 reference

31 July 2017

Thomas E. Cheatham

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

25 March 2024

language of work or name

English

0 references

publication date

1 November 2003

1 reference

full work available at URL

31 July 2017

http://www.cell.com/article/S0006349503747109/pdf

file format

Portable Document Format

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

https://europepmc.org/articles/PMC1303568

25 March 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

https://europepmc.org/articles/PMC1303568?pdf=render

25 March 2024

file format

Portable Document Format

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14581192

https://api.elsevier.com/content/article/PII:S0006349503747109?httpAccept=text/xml

25 March 2024

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(03)74710-9

https://api.elsevier.com/content/article/PII:S0006349503747109?httpAccept=text/plain

25 March 2024

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(03)74710-9

25 March 2024

1 reference

31 July 2017

85

1 reference

31 July 2017

5

1 reference

31 July 2017

2872-2883

1 reference

An optimized potential function for the calculation of nucleic acid interaction energies I. base stacking

31 July 2017

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

5 July 2018

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

7 January 2021

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

inferred from DOI database lookup

7 January 2021

based on heuristic

High-throughput approach for detection of DNA bending and flexibility based on cyclization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Hidden Markov models from molecular dynamics simulations on DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Global structure and mechanical properties of a 10-bp nucleosome positioning motif

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Molecular dynamics simulation of nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

A-form conformational motifs in ligand-bound DNA structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Sequence-dependent dynamics in duplex DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Nucleic acids: theory and computer simulation, Y2K.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Sequence-dependent DNA structure: tetranucleotide conformational maps

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

From atomic to mesoscopic descriptions of the internal dynamics of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Resolving the discrepancies among nucleic acid conformational analyses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Simulating DNA at low resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Modeling superhelical DNA: recent analytical and dynamic approaches.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

The effects of sequence context on base dynamics at TpA steps in DNA studied by NMR.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Sequence-structure relationships in DNA oligomers: a computational approach.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

Sequence-dependent elastic properties of DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

DNA: an extensible molecule.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303568

From the sequence to the superstructural properties of DNAs

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

7 January 2021

Left-handed DNA helices

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Molecular dynamics with coupling to an external bath

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Collective motion artifacts arising in long-duration molecular dynamics simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

B-DNA twisting correlates with base-pair morphology.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Molecular Dynamics Simulation of DNA Stretching Is Consistent with the Tension Observed for Extension and Strand Separation and Predicts a Novel Ladder Structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Modelling DNA conformational mechanics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

NMR evidence for base dynamics at all TpA steps in DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Modeling DNA deformations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Torsional constant of 27-mer DNA oligomers of different sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Elastic stability of DNA configurations. I. General theory

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Identification and characterization of genomic nucleosome-positioning sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

A smooth particle mesh Ewald method

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974710-9

inferred from DOI database lookup

7 January 2021

based on heuristic

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

53

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(03)74710-9

25 March 2024

Identifiers

1 reference

31 July 2017

1 reference

31 July 2017

1 reference