(Q34171203)

31 July 2017

title

Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints (English)

1 reference

31 July 2017

Tzou WS

1

1 reference

31 July 2017

Hwang MJ

series ordinal

2

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 September 1999

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31 July 2017

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31 July 2017

volume

77

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31 July 2017

issue

3

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31 July 2017

page(s)

1191-1205

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Thermodynamics of sequence-specific protein-DNA interactions.

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Structure determination and analysis of helix parameters in the DNA decamer d(CATGGCCATG)2 comparison of results from NMR and crystallography

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

DNA bending: the prevalence of kinkiness and the virtues of normality

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

The transactivation region of the fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

DNA recognition and bending

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Location, degree, and direction of DNA bending associated with the Hin recombinational enhancer sequence and Fis-enhancer complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Crystal studies of B-DNA: the answers and the questions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

A model for Fis N-terminus and Fis-invertase recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Structure model of a complex between the factor for inversion stimulation (FIS) and DNA: modeling protein-DNA complexes with dyad symmetry and known protein structures.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Computational methods for biomolecular docking.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Towards an understanding of protein-DNA recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Structure of the Escherichia coli Fis-DNA complex probed by protein conjugated with 1,10-phenanthroline copper(I) complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

DNA-binding proteins as site-specific nucleases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Electrostatic deformation of DNA by a DNA-binding protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Recognition of a DNA operator by the repressor of phage 434: a view at high resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Fis binding to the recombinational enhancer of the Hin DNA inversion system

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Defining the structure of irregular nucleic acids: conventions and principles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

DNA recognition by proteins with the helix-turn-helix motif

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Three-dimensional structure of the E. coli DNA-binding protein FIS.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Static and statistical bending of DNA evaluated by Monte Carlo simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Identification of two functional regions in Fis: the N-terminus is required to promote Hin-mediated DNA inversion but not lambda excision

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Transcription factors: structural families and principles of DNA recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Modelling repressor proteins docking to DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Predictive docking of protein-protein and protein-DNA complexes.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Role of base-backbone and base-base interactions in alternating DNA conformations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

The bacteriophage 434 right operator. Roles of O(R)1, O(R)2 and O(R)3.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

MONTY: a Monte Carlo approach to protein-DNA recognition.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300411

CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Structural aspects of protein-DNA interactions as revealed by conversion of the interacting protein into a sequence-specific cross-linking agent or a chemical nuclease

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Definitions and nomenclature of nucleic acid structure parameters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

B-DNA twisting correlates with base-pair morphology.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Topological measurement of protein-induced DNA bend angles

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Crystallographic studies of protein-nucleic acid interaction: catabolite gene activator protein and the large fragment of DNA polymerase I.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Binding geometry of alpha-helices that recognize DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

DNA recognition and superstructure formation by helix-turn-helix proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2976971-7

10.1016/S0006-3495(99)76971-7

7 January 2021

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference