ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences. (Q30329286)

18 June 2017

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

1 reference

18 June 2017

Lafontaine I

1

1 reference

PubMed ID

11754342

18 June 2017

Lavery R

series ordinal

2

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18 June 2017

1 January 2000

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18 June 2017

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18 June 2017

56

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18 June 2017

4

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18 June 2017

292-310

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Bent helical structure in kinetoplast DNA.

18 June 2017

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Evidence for the existence of stable curvature of DNA in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Activation of transcription at sigma 54-dependent promoters on linear templates requires intrinsic or induced bending of the DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Functional replacement of a protein-induced bend in a DNA recombination site

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

DNA bending and its relation to nucleosome positioning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The locus of sequence-directed and protein-induced DNA bending

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

DNA curving and bending in protein-DNA recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The basics of basal transcription by RNA polymerase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The TATA box binding protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Transcription factors: structural families and principles of DNA recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Biochemistry and structural biology of transcription factor IID (TFIID)

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

In vivo sequence requirements of the SV40 early promoter region

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Cloning and functional analysis of the TATA binding protein from Sulfolobus shibatae

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Co-crystal structure of TBP recognizing the minor groove of a TATA element

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Crystal structure of a yeast TBP/TATA-box complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

2.1 A resolution refined structure of a TATA box-binding protein (TBP)

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Crystal structure of a human TATA box-binding protein/TATA element complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

How proteins recognize the TATA box

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The crystal structure of a hyperthermophilic archaeal TATA-box binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Affinity, stability and polarity of binding of the TATA binding protein governed by flexure at the TATA Box.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Signals for TBP/TATA box recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A-Tract bending: insights into experimental structures by computational models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Eukaryotic promoter recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The density of transcriptional elements in promoter and non-promoter sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The biology of eukaryotic promoter prediction--a review

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

21 January 2018

Structure of Chromatin

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Toward a unified model of chromatin folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Structure, dynamics, and function of chromatin in vitro.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Structure of the nucleosome core particle at 7 Å resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Crystal structure of the nucleosome core particle at 2.8 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

DNA binding within the nucleosome core

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Nucleosome packaging and nucleosome positioning of genomic DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The pitch of chromatin DNA is reflected in its nucleotide sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Sequence periodicities in chicken nucleosome core DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Regulation of gene expression by nucleosomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Differential nucleosome positioning on Xenopus oocyte and somatic 5 S RNA genes determines both TFIIIA and H1 binding: a mechanism for selective H1 repression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The mouse mammary tumour virus promoter positioned on a tetramer of histones H3 and H4 binds nuclear factor 1 and OTF1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

DNA structure in human RNA polymerase II promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A DNA structural atlas for Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Genes and the physics of the DNA double-helix.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The physics of DNA and the annotation of the Plasmodium falciparum genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Optimization of nucleic acid sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Collective variable modelling of nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

DNA: an extensible molecule.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Unusual DNA conformations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Mean-field minimization methods for biological macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Designing the hydrophobic core of Thermus flavus malate dehydrogenase based on side-chain packing

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Computational method to reduce the search space for directed protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The molecular origin of DNA-drug specificity in netropsin and distamycin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Protein fold recognition by threading: comparison of algorithms and analysis of results.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG)

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Energetics of Z-DNA formation in poly d(A-T), poly d(G-C), and poly d(A-C) poly d(G-T).

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Sequence dependence of the curvature of DNA: a test of the phasing hypothesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Origins of netropsin binding affinity and specificity: correlations of thermodynamic and structural data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

TRANSFAC: a database on transcription factors and their DNA binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Compilation and analysis of eukaryotic POL II promoter sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The eukaryotic promoter database (EPD).

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

A General Approach to the Optimization of the Conformation of Ring Molecules with an Application to Valinomycin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

Sequence-directed curvature of DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282000%2956%3A4%3C292%3A%3AAID-BIP10028%3E3.0.CO%3B2-9

10.1002/1097-0282(2000)56:4<292::AID-BIP10028>3.0.CO;2-9

21 January 2018

Identifiers

DOI

1 reference

18 June 2017

1 reference

PubMed ID

11754342