Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors (Q43063731)

13 November 2017

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors (English)

1 reference

13 November 2017

Jiajian Liu

1

1 reference

13 November 2017

Gary D Stormo

series ordinal

2

1 reference

13 November 2017

language of work or name

English

0 references

publication date

27 June 2008

1 reference

13 November 2017

1 reference

13 November 2017

24

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13 November 2017

17

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13 November 2017

1850-1857

1 reference

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

13 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Connectivity in the yeast cell cycle transcription network: inferences from neural networks

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Pfam: clans, web tools and services

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Ab initio prediction of transcription factor targets using structural knowledge

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

enoLOGOS: a versatile web tool for energy normalized sequence logos

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Improved prediction of signal peptides: SignalP 3.0

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

An overview of the structures of protein-DNA complexes

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

DNA recognition by Cys2His2 zinc finger proteins

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

New tools and resources for analysing protein structures and their interactions

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

How Cro and lambda-repressor distinguish between operators: the structural basis underlying a genetic switch

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

A molecular code dictates sequence-specific DNA recognition by homeodomains.

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

26 May 2018

Protein-DNA recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Protein-DNA interaction. No code for recognition

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Predicting the secondary structure of globular proteins using neural network models

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Sequence-specific recognition of double helical nucleic acids by proteins

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Position dependencies in transcription factor binding sites

26 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Non-additivity in protein-DNA binding

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Modeling within-motif dependence for transcription factor binding site predictions

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2732218

Physical basis of a protein-DNA recognition code

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18586699

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

PubMed

https://pubmed.ncbi.nlm.nih.gov/18586699

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18586699

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTN331

1 reference

journals/bioinformatics/LiuS08

13 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

13 November 2017

PubMed publication ID

18586699

1 reference