Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein (Q24811831)

4 July 2017

Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein (English)

1 reference

4 July 2017

Jiajian Liu

1

1 reference

PubMed ID

16014175

4 July 2017

Gary D Stormo

series ordinal

2

1 reference

PubMed ID

16014175

4 July 2017

language of work or name

English

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publication date

13 July 2005

1 reference

4 July 2017

1 reference

4 July 2017

6

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4 July 2017

1

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page(s)

176

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-6-176

4 July 2017

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cites work

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

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Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage

7 April 2017

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Sequence logos: a new way to display consensus sequences

7 April 2017

1 reference

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Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes

7 April 2017

1 reference

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High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Design and selection of novel Cys2His2 zinc finger proteins

7 April 2017

2 references

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Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

DNA recognition by Cys2His2 zinc finger proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Additivity in protein-DNA interactions: how good an approximation is it?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Rapid, high-throughput engineering of sequence-specific zinc finger DNA-binding proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Artificial zinc finger peptides: creation, DNA recognition, and gene regulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Structure-based prediction of DNA target sites by regulatory proteins.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Specificity, free energy and information content in protein-DNA interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Measurement of nucleic acid concentrations using the DyNA Quant and the GeneQuant.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Zinc finger phage: affinity selection of fingers with new DNA-binding specificities

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Stereochemical basis of DNA recognition by Zn fingers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Length-encoded multiplex binding site determination: application to zinc finger proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

DNA recognition code of transcription factors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Quantitative analysis of the relationship between nucleotide sequence and functional activity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Toward rules relating zinc finger protein sequences and DNA binding site preferences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Analyzing protein-DNA recognition mechanisms.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Probabilistic code for DNA recognition by proteins of the EGR family.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Validated zinc finger protein designs for all 16 GNN DNA triplet targets

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

The ClpX protein of Bacillus subtilis indirectly influences RNA polymerase holoenzyme composition and directly stimulates sigma-dependent transcription.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

Displaying the information contents of structural RNA alignments: the structure logos.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1184061

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

28 November 2018

1 reference

12 December 2020

Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor

1 reference

12 December 2020

Physical basis of a protein-DNA recognition code

1 reference

12 December 2020

Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1

1 reference

12 December 2020

Binding studies with mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the Zif268 zinc finger-DNA complex

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-6-176

1 reference

4 July 2017

journals/bmcbi/LiuS05

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

4 July 2017

1 reference

PubMed ID

16014175