Assessment of the optimization of affinity and specificity at protein-DNA interfaces (Q37215395)

19 August 2017

Assessment of the optimization of affinity and specificity at protein-DNA interfaces (English)

1 reference

19 August 2017

Justin Ashworth

1

0 references

David Baker

object named as

David Baker

series ordinal

2

0 references

language of work or name

English

0 references

publication date

23 April 2009

1 reference

19 August 2017

Nucleic Acids Research

1 reference

19 August 2017

37

1 reference

19 August 2017

10

1 reference

19 August 2017

e73

1 reference

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Coevolution of a Homing Endonuclease and Its Host Target Sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Computational redesign of endonuclease DNA binding and cleavage specificity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Homing endonuclease structure and function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

DNA recognition by Cys2His2 zinc finger proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

6 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=2691843

Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Site-directed mutagenesis of phosphate-contacting amino acids of bovine pancreatic deoxyribonuclease I.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Specific binding by EcoRV endonuclease to its DNA recognition site GATATC.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Crystal structure of a yeast TBP/TATA-box complex

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Zinc finger phage: affinity selection of fingers with new DNA-binding specificities

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Alanine scanning site-directed mutagenesis of the zinc fingers of transcription factor ADR1: residues that contact DNA and that transactivate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Transcription factors: structural families and principles of DNA recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Replacement of invariant bZip residues within the basic region of the yeast transcriptional activator GCN4 can change its DNA binding specificity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Mutagenesis of the DNA binding residues in bovine pancreatic DNase 1: an investigation into the mechanism of sequence discrimination by a sequence selective nuclease

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Sequence-dependent variation in the conformation of DNA

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Determination of the base recognition positions of zinc fingers from sequence analysis

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691843

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

3 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19389725

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

EcoRV restriction endonuclease binds all DNA sequences with equal affinity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19389725

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/19389725

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKP242

1 reference

19 August 2017

1 reference

19 August 2017

1 reference

PMCID

2691843