(Q43116314)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Rosa Di Felice

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

6

Tahereh Ghane

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

author name string

Tianyin Zhou

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Lin Yang

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Iris Dror

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Ana Carolina Dantas Machado

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Remo Rohs

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

language of work or name

English

0 references

publication date

22 May 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

volume

41

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

issue

Web Server issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

page(s)

W56-62

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 3.0 Unported

1 March 2020

copyright license

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Probing DNA shape and methylation state on a genomic scale with DNase I.

1 reference

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Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Origins of specificity in protein-DNA recognition.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Electrostatic interactions between arginines and the minor groove in the nucleosome.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

The role of DNA shape in protein-DNA recognition

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Nuance in the double-helix and its role in protein-DNA recognition.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Local DNA topography correlates with functional noncoding regions of the human genome

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Nucleosome organization in the Drosophila genome.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Towards a molecular dynamics consensus view of B-DNA flexibility

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Sequence-dependent DNA deformability studied using molecular dynamics simulations

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Unraveling proteins: a molecular mechanics study

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

The pitch of chromatin DNA is reflected in its nucleotide sequence

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Sequence periodicities in chicken nucleosome core DNA.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Defining the structure of irregular nucleic acids: conventions and principles

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692085

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

15 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT437

Molecular Dynamics of DNA: Comparison of Force Fields and Terminal Nucleotide Definitions

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23703209

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Optical properties of triplex DNA from time-dependent density functional theory

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23703209

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23703209

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT437

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

journals/nar/ZhouYLDMGFR13

1 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

PubMed publication ID

23703209

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23703209%20AND%20SRC:MED&resulttype=core&format=json