(Q39117389)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

title

Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

Ralf Everaers

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

author name string

Lars Wolff

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

language of work or name

English

0 references

publication date

11 October 2006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

number of pages

12

1 reference

inferred from page(s)

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

volume

34

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

issue

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

page(s)

5638-5649

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

Computational redesign of endonuclease DNA binding and cleavage specificity

20 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Protein-DNA binding specificity predictions with structural models

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Recognition of DNA structure by 434 repressor

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

The phage 434 OR2/R1-69 complex at 2.5 A resolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Recognition of a DNA operator by the repressor of phage 434: a view at high resolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Sequence logos: a new way to display consensus sequences

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

DNA recognition code of transcription factors

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Looking into DNA recognition: zinc finger binding specificity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Protein-DNA interaction. No code for recognition

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Weight matrices for protein-DNA binding sites from a single co-crystal structure

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

Analyzing protein-DNA recognition mechanisms.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

DNA sequence and structure: direct and indirect recognition in protein-DNA binding

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

The role of DNA bending in Cro protein-DNA interactions.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1636474

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

21 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL683

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%2FGKL683

Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL683

DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 represser

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKL683

Influence of DNA stiffness in protein-DNA recognition

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17038333

12 December 2020

inferred from PubMed ID database lookup

Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17038333

12 December 2020

inferred from PubMed ID database lookup

Structural and thermodynamic strategies for site-specific DNA binding proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17038333

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1093/NAR/GKL683

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17038333%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

1 reference