(Q35040989)

6 August 2017

Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants (English)

1 reference

6 August 2017

Christian A Grove

2

0 references

Federico De Masi

Federico De Masi

1

0 references

Andreu Alibés

Andreu Alibés

4

0 references

Stephen S. Gisselbrecht

Stephen S Gisselbrecht

5

0 references

Marian Walhout

8

Albertha J M Walhout

1 reference

6 August 2017

7

Martha L Bulyk

1 reference

6 August 2017

Anastasia Vedenko

3

1 reference

PubMed ID

21335608

6 August 2017

Luis Serrano

6

1 reference

PubMed ID

21335608

6 August 2017

language of work or name

English

0 references

publication date

18 February 2011

1 reference

6 August 2017

11

1 reference

based on heuristic

inferred from page(s)

published in

Nucleic Acids Research

1 reference

6 August 2017

39

1 reference

6 August 2017

11

1 reference

6 August 2017

4553-4563

1 reference

Creative Commons Attribution-NonCommercial 2.5 Generic

6 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example

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Experimental determination of the evolvability of a transcription factor

8 July 2018

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A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors

8 July 2018

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Diversity and complexity in DNA recognition by transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions

8 July 2018

1 reference

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Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

8 July 2018

1 reference

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UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

8 July 2018

1 reference

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Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Crystal structure of E47-NeuroD1/beta2 bHLH domain-DNA complex: heterodimer selectivity and DNA recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Delta-Notch--and then? Protein interactions and proposed modes of repression by Hes and Hey bHLH factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

A systems approach to measuring the binding energy landscapes of transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping.

8 July 2018

1 reference

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Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

DBD: a transcription factor prediction database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

The FoldX web server: an online force field

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Looking into DNA recognition: zinc finger binding specificity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

A HANDful of questions: the molecular biology of the heart and neural crest derivatives (HAND)-subclass of basic helix-loop-helix transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Vertebrate hairy and Enhancer of split related proteins: transcriptional repressors regulating cellular differentiation and embryonic patterning

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Protein interaction mapping in C. elegans using proteins involved in vulval development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Establishment of distinct MyoD, E2A, and twist DNA binding specificities by different basic region-DNA conformations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

A helix propensity scale based on experimental studies of peptides and proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

A natural classification of the basic helix-loop-helix class of transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Structure and function of the b/HLH/Z domain of USF

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Comparison of DNA binding across protein superfamilies.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Transcription factor functionality and transcription regulatory networks

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Molecular architecture of the DNA-binding region and its relationship to classification of basic helix-loop-helix proteins

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

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

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

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

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113581

Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation

25 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21335608

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An analysis of information content present in protein-DNA interactions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21335608

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR070

1 reference

6 August 2017

1 reference

6 August 2017

1 reference

PubMed ID

21335608