Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor (Q37346433)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15289576%20AND%20SRC:MED&resulttype=core&format=json

31 December 2019

title

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

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31 December 2019

1

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31 December 2019

author name string

Joshua SungWoo Yang

series ordinal

2

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31 December 2019

Gary D Stormo

series ordinal

3

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31 December 2019

language of work or name

English

0 references

publication date

2 August 2004

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31 December 2019

published in

Nucleic Acids Research

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31 December 2019

volume

32

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31 December 2019

issue

13

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31 December 2019

page(s)

4026-4032

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

31 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=506813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Mining genome databases to identify and understand new gene regulatory systems.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Genome-wide location and function of DNA binding proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

An overview of the structures of protein-DNA complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

DNA binding sites: representation and discovery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Quantitative specificity of the Mnt repressor

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Additivity of mutant effects assessed by binomial mutagenesis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

DNA recognition by beta-sheets in the Arc repressor-operator crystal structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Sequence logos: a new way to display consensus sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

DNA recognition code of transcription factors

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Protein-DNA interaction. No code for 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=506813

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

Changing the DNA-binding specificity of a repressor

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=506813

One-hybrid systems for detecting protein-DNA interactions

20 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15289576

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15289576

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Physical basis of a protein-DNA recognition code

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15289576

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKH729

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15289576%20AND%20SRC:MED&resulttype=core&format=json

31 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15289576%20AND%20SRC:MED&resulttype=core&format=json

31 December 2019

PubMed publication ID

15289576

1 reference