Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites (Q28476187)

From Wikidata

Jump to navigation Jump to search

scientific article

edit

Language	Label	Description	Also known as
English	Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites	scientific article

Statements

instance of

scholarly article

0 references

title

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites (English)

0 references

author

William S Hlavacek

object named as

William S Hlavacek

series ordinal

2

0 references

author name string

Amy L Bauer

series ordinal

1

0 references

Pat J Unkefer

series ordinal

3

0 references

Fangping Mu

series ordinal

4

0 references

language of work or name

English

0 references

publication date

18 November 2010

0 references

published in

PLOS Computational Biology

0 references

volume

6

0 references

issue

11

0 references

page(s)

e1001007

0 references

copyright license

Creative Commons Attribution 4.0 International

start time

18 November 2010

1 reference

stated in

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo

2 references

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

6 April 2017

From genomics to chemical genomics: new developments in KEGG

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

Protein-DNA binding specificity predictions with structural models

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

Scalable molecular dynamics with NAMD

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

Ab initio prediction of transcription factor targets using structural knowledge

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

MATCH: A tool for searching transcription factor binding sites in DNA sequences

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

DNA binding sites: representation and discovery

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

19 March 2017

MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

7 April 2017

MatInspector and beyond: promoter analysis based on transcription factor binding sites

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

7 April 2017

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

7 April 2017

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Recent advances in the study of nucleic acid flexibility by molecular dynamics

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Connecting protein structure with predictions of regulatory sites.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Protein-DNA recognition patterns and predictions.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Toward an atomistic model for predicting transcription-factor binding sites

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Simulation and modeling of nucleic acid structure, dynamics and interactions

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

Predicting indirect readout effects in protein-DNA interactions

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

A biophysical approach to transcription factor binding site discovery

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

A standard reference frame for the description of nucleic acid base-pair geometry.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

29 September 2017

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

2 June 2018

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2987836

retrieved

2 June 2018

Design principles for regulator gene expression in a repressible gene circuit

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001007

retrieved

21 January 2018

Comparative analysis of methods for representing and searching for transcription factor binding sites

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001007

retrieved

21 January 2018

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

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001007

retrieved

21 January 2018

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001007

retrieved

21 January 2018

An introduction to ROC analysis

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001007

retrieved

21 January 2018

Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001007

retrieved

21 January 2018

Identifiers

DOI

10.1371/JOURNAL.PCBI.1001007

0 references

DBLP publication ID

journals/ploscb/BauerHUM10

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

PMC publication ID

2987836

0 references

PubMed publication ID

21124945

0 references

ResearchGate publication ID

49652008

0 references

 

Sitelinks

Wikipedia(0 entries)

edit

Wikibooks(0 entries)

edit

Wikinews(0 entries)

edit

Wikiquote(0 entries)

edit

Wikisource(0 entries)

edit

Wikiversity(0 entries)

edit

Wikivoyage(0 entries)

edit

Wiktionary(0 entries)

edit

Multilingual sites(0 entries)

edit

Retrieved from "https://www.wikidata.org/w/index.php?title=Q28476187&oldid=1869862587"