(Q42027009)

15 October 2017

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins (English)

1 reference

15 October 2017

Anton V Persikov

1

1 reference

PMCID

3874201

15 October 2017

Mona Singh

series ordinal

2

1 reference

15 October 2017

3 October 2013

1 reference

15 October 2017

Nucleic Acids Research

1 reference

15 October 2017

42

1 reference

15 October 2017

1

1 reference

15 October 2017

97-108

1 reference

Creative Commons Attribution 3.0 Unported

15 October 2017

start time

10 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

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DNA-binding specificities of human transcription factors

5 June 2018

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FlyBase: improvements to the bibliography

5 June 2018

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Architecture of the human regulatory network derived from ENCODE data

5 June 2018

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Recognition models to predict DNA-binding specificities of homeodomain proteins

5 June 2018

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An optimized two-finger archive for ZFN-mediated gene targeting

5 June 2018

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Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

5 June 2018

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An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces

5 June 2018

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5 June 2018

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Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Identification of functional elements and regulatory circuits by Drosophila modENCODE

5 June 2018

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FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

5 June 2018

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Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination

5 June 2018

1 reference

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JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

5 June 2018

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Diversity and complexity in DNA recognition by transcription factors

5 June 2018

1 reference

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A census of human transcription factors: function, expression and evolution

5 June 2018

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

High-resolution DNA-binding specificity analysis of yeast transcription factors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Predicting DNA recognition by Cys2His2 zinc finger proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Progress and prospects: zinc-finger nucleases as gene therapy agents

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

A novel Bayesian DNA motif comparison method for clustering and retrieval

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Unexpected failure rates for modular assembly of engineered zinc fingers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Eukaryotic transcription factor binding sites--modeling and integrative search methods

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

STAMP: a web tool for exploring DNA-binding motif similarities

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Quantifying similarity between motifs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Protein-DNA binding specificity predictions with structural models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Ab initio prediction of transcription factor targets using structural knowledge

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Toward an atomistic model for predicting transcription-factor binding sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

WebLogo: A Sequence Logo Generator

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Combining phylogenetic data with co-regulated genes to identify regulatory motifs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Multifunctional zinc finger proteins in development and disease

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Three classes of C2H2 zinc finger proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

DNA recognition by Cys2His2 zinc finger proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

DNA binding sites: representation and discovery

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

lola encodes a putative transcription factor required for axon growth and guidance in Drosophila

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

DNA recognition code of transcription factors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

Sequence logos: a new way to display consensus sequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

The tramtrack gene encodes a Drosophila finger protein that interacts with the ftz transcriptional regulatory region and shows a novel embryonic expression pattern

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

ZIFIBI: Prediction of DNA binding sites for zinc finger proteins.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

A simple physical model for the prediction and design of protein-DNA interactions.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874201

17 August 2018

Identifiers

DOI

10.1093/NAR/GKT890

1 reference

15 October 2017

1 reference

15 October 2017

1 reference

PMCID

3874201