A new method for evaluating the specificity of indirect readout in protein-DNA recognition (Q36280589)

13 August 2017

A new method for evaluating the specificity of indirect readout in protein-DNA recognition (English)

1 reference

13 August 2017

Satoshi Yamasaki

1

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13 August 2017

Tohru Terada

2

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13 August 2017

Hidetoshi Kono

3

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13 August 2017

Kentaro Shimizu

4

1 reference

13 August 2017

Akinori Sarai

5

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13 August 2017

language of work or name

English

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publication date

22 May 2012

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13 August 2017

Nucleic Acids Research

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13 August 2017

40

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13 August 2017

17

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13 August 2017

e129

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Creative Commons Attribution-NonCommercial 3.0 Unported

13 August 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/3458528

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Protein-DNA recognition patterns and predictions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

A-form conformational motifs in ligand-bound DNA structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

30 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

Degenerate DNA recognition by I-PpoI endonuclease.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

The Brachyury gene encodes a novel DNA binding protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

Sequence logos: a new way to display consensus sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

Sequence-dependent DNA deformability studied using molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

A generalized conformational energy function of DNA derived from molecular dynamics simulations.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

DNA binding specificity studies of four ETS proteins support an indirect read-out mechanism of protein-DNA recognition.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458528

A Mathematical Theory of Communication

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS462

Probing the physical basis for trp repressor-operator recognition

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS462

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS462

21 January 2018

Identifiers

DOI

10.1093/NAR/GKS462

1 reference

13 August 2017

1 reference

13 August 2017

PubMed publication ID

22618872

1 reference