Connecting protein structure with predictions of regulatory sites. (Q30361132)

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29 December 2019

title

Connecting protein structure with predictions of regulatory sites (English)

1 reference

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protein structure prediction

29 December 2019

main subject

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language of work or name

English

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publication date

16 April 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17438293%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

29 December 2019

published in

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29 December 2019

volume

104

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29 December 2019

issue

17

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29 December 2019

page(s)

7068-7073

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Informative priors based on transcription factor structural class improve de novo motif discovery

29 December 2019

cites work

1 reference

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Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

3 June 2018

1 reference

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An improved map of conserved regulatory sites for Saccharomyces cerevisiae

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

DBD: a transcription factor prediction database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Protein-DNA binding specificity predictions with structural models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Ab initio prediction of transcription factor targets using structural knowledge

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

DIP-chip: rapid and accurate determination of DNA-binding specificity.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Transcriptional regulatory code of a eukaryotic genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

MotifPrototyper: a Bayesian profile model for motif families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Swapping functional specificity of a MADS box protein: residues required for Arg80 regulation of arginine metabolism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Structural analysis of conserved base pairs in protein-DNA complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Genome-wide location and function of DNA binding proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

An overview of the structures of protein-DNA complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Structural basis for the diversity of DNA recognition by bZIP transcription factors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress.

3 June 2018

1 reference

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SURVEY AND SUMMARY: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes

3 June 2018

1 reference

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Protein-DNA interactions: A structural analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Assembly of a bZIP-bHLH transcription activation complex: formation of the yeast Cbf1-Met4-Met28 complex is regulated through Met28 stimulation of Cbf1 DNA binding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Characterization of the DNA target site for the yeast ARGR regulatory complex, a sequence able to mediate repression or induction by arginine

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

DNA recognition by GAL4: structure of a protein-DNA complex.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Transcription factors: structural families and principles of DNA recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1855371

Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701356104

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701356104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701356104

Sequence features of DNA binding sites reveal structural class of associated transcription factor

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701356104

Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0701356104

Structural basis of Hox specificity

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17438293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17438293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Linkers made to measure

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17438293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0701356104

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17438293%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17438293%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

PubMed publication ID

17438293

1 reference