(Q30329286)

18 June 2017

title

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

1 reference

18 June 2017

Lafontaine I

1

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18 June 2017

Lavery R

series ordinal

2

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18 June 2017

publication date

1 January 2000

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18 June 2017

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18 June 2017

volume

56

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18 June 2017

issue

4

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18 June 2017

page(s)

292-310

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Bent helical structure in kinetoplast DNA.

18 June 2017

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21 January 2018

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21 January 2018

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

21 January 2018

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21 January 2018

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

21 January 2018

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DNA curving and bending in protein-DNA recognition

21 January 2018

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

21 January 2018

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The basics of basal transcription by RNA polymerase II.

21 January 2018

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The TATA box binding protein.

21 January 2018

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Transcription factors: structural families and principles of DNA recognition

21 January 2018

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Biochemistry and structural biology of transcription factor IID (TFIID)

21 January 2018

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In vivo sequence requirements of the SV40 early promoter region

21 January 2018

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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

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Crystal structure of a yeast TBP/TATA-box complex

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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How proteins recognize the TATA box

21 January 2018

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

21 January 2018

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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

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

21 January 2018

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Signals for TBP/TATA box recognition

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Eukaryotic promoter recognition

21 January 2018

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

21 January 2018

1 reference

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The biology of eukaryotic promoter prediction--a review

21 January 2018

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21 January 2018

Structure of Chromatin

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21 January 2018

1 reference

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Toward a unified model of chromatin folding

21 January 2018

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Structure, dynamics, and function of chromatin in vitro

21 January 2018

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

21 January 2018

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Structure of the nucleosome core particle at 7 Å resolution

21 January 2018

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Crystal structure of the nucleosome core particle at 2.8 A resolution

21 January 2018

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DNA binding within the nucleosome core

21 January 2018

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Nucleosome packaging and nucleosome positioning of genomic DNA

21 January 2018

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The pitch of chromatin DNA is reflected in its nucleotide sequence

21 January 2018

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Sequence periodicities in chicken nucleosome core DNA.

21 January 2018

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

21 January 2018

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

21 January 2018

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Regulation of gene expression by nucleosomes

21 January 2018

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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

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

21 January 2018

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

21 January 2018

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

21 January 2018

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DNA structure in human RNA polymerase II promoters

21 January 2018

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A DNA structural atlas for Escherichia coli

21 January 2018

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Genes and the physics of the DNA double-helix.

21 January 2018

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

21 January 2018

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Optimization of nucleic acid sequences

21 January 2018

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Collective variable modelling of nucleic acids

21 January 2018

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

21 January 2018

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

21 January 2018

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DNA: an extensible molecule.

21 January 2018

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Unusual DNA conformations.

21 January 2018

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Mean-field minimization methods for biological macromolecules

21 January 2018

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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

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Computational method to reduce the search space for directed protein evolution

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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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

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21 January 2018

1 reference

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

21 January 2018

1 reference

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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

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

21 January 2018

1 reference

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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

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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Compilation and analysis of eukaryotic POL II promoter sequences

21 January 2018

1 reference

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The eukaryotic promoter database (EPD).

21 January 2018

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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

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

21 January 2018

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

21 January 2018

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

21 January 2018

1 reference

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

21 January 2018

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

21 January 2018

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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