(Q40937533)

25 September 2017

Looking into DNA recognition: zinc finger binding specificity (English)

1 reference

25 September 2017

Guillaume Paillard

1

1 reference

PMCID

545445

25 September 2017

Cyril Deremble

series ordinal

2

1 reference

PMCID

545445

25 September 2017

Richard Lavery

series ordinal

3

1 reference

25 September 2017

21 December 2004

1 reference

25 September 2017

Nucleic Acids Research

1 reference

25 September 2017

32

1 reference

25 September 2017

6673-6682

1 reference

25 September 2017

22

1 reference

Hidden Markov models from molecular dynamics simulations on DNA.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

25 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=545445

Engineering polydactyl zinc-finger transcription factors

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Optimization of nucleic acid sequences

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Synergy between adjacent zinc fingers in sequence-specific DNA recognition

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Satisfying hydrogen bonding potential in proteins

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

DNA-binding specificity of NGFI-A and related zinc finger transcription factors

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

DNA recognition code of transcription factors

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Information content of binding sites on nucleotide sequences

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

DNA binding site of the growth factor-inducible protein Zif268

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Sequence logos: a new way to display consensus sequences

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Sequence-specific recognition of double helical nucleic acids by proteins

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Sequence dependence of DNA conformational flexibility.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Analyzing protein-DNA recognition mechanisms.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

DNA sequence and structure: direct and indirect recognition in protein-DNA binding

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545445

Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15613596

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/15613596

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15613596

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKH1003

1 reference

25 September 2017

1 reference

25 September 2017

1 reference

PMCID

545445