Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

scientific article published in December 2015

Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence is …
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scholarly articleQ13442814

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P819ADS bibcode2015PLoSO..1043760I
P818arXiv ID1511.02026
P356DOI10.1371/JOURNAL.PONE.0143760
P724Internet Archive IDarxiv-1511.02026
P932PMC publication ID4666469
P698PubMed publication ID26624614
P5875ResearchGate publication ID283619509

P50authorNaoaki SakamotoQ63966765
P2093author name stringAkinori Awazu
Hiraku Nishimori
Shuhei Isami
P2860cites workStructure of a B-DNA dodecamer: conformation and dynamicsQ24635075
A genomic code for nucleosome positioningQ24650238
The structure of a stable intermediate in the A left-right-arrow B DNA helix transitionQ27621551
Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structuresQ27655484
Re-refinement of the B-dodecamer d(CGCGAATTCGCG) with a comparative analysis of the solvent in it and in the Z-hexamer d(5BrCG5BrCG5BrCG)Q27728565
G . T base-pairs in a DNA helix: the crystal structure of d(G-G-G-G-T-C-C-C)Q27729054
Sequence-dependent microheterogeneity of Z-DNA: the crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG)Q27730242
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structuresQ27860547
Looping and interaction between hypersensitive sites in the active beta-globin locusQ28198196
Capturing chromosome conformationQ28201750
Insulators: exploiting transcriptional and epigenetic mechanismsQ28257767
Topological domains in mammalian genomes identified by analysis of chromatin interactionsQ28264221
iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical propertiesQ28484598
Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamicsQ28536143
Dynamic regulation of nucleosome positioning in the human genomeQ29615046
DNA sequence-dependent deformability deduced from protein-DNA crystal complexesQ29616629
Network-based models as tools hinting at nonevident protein functionalityQ30414102
Sequence-dependent motions of DNA: a normal mode analysis at the base-pair levelQ30476422
Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations.Q30497624
G+C content dominates intrinsic nucleosome occupancyQ33520380
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.Q33566434
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteinsQ33718901
Anisotropy of fluctuation dynamics of proteins with an elastic network modelQ33931550
ICM Web: the interactive chromatin modeling web serverQ33957654
DNA Basepair Step Deformability Inferred from Molecular Dynamics SimulationsQ34183456
The ABCs of molecular dynamics simulations on B-DNA, circa 2012.Q34323341
A coarse grain model for DNA.Q51053784
A sequence-dependent rigid-base model of DNA.Q51258695
Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.Q51530772
Interpreting correlated motions using normal mode analysis.Q51928962
DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.Q52390733
Coarse-grained modeling of DNA curvature.Q53399728
DNA shape dominates sequence affinity in nucleosome formation.Q53399967
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic AnalysisQ56688821
Harmonicity in slow protein dynamicsQ58008915
A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chiralityQ62660859
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction dataQ34343663
Chemically accurate coarse graining of double-stranded DNA.Q34377420
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNAQ34489622
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNAQ34510040
A high-resolution atlas of nucleosome occupancy in yeastQ34688532
Coarse-grained normal mode analysis in structural biologyQ34694568
NAFlex: a web server for the study of nucleic acid flexibility.Q34728020
Protecting against promiscuity: the regulatory role of insulatorsQ35060057
A coarse-grain three-site-per-nucleotide model for DNA with explicit ionsQ35566156
A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion MethodQ35847165
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Q36002495
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.Q36129144
Insulators and promoters: closer than we thinkQ36337521
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.Q36475375
Chromatin insulatorsQ36585889
Towards a molecular dynamics consensus view of B-DNA flexibilityQ36633176
Multiscale modeling of nucleic acids: insights into DNA flexibilityQ36923784
The hierarchy of the 3D genomeQ37090603
Recent advances in the study of nucleic acid flexibility by molecular dynamicsQ37096358
Protein elastic network models and the ranges of cooperativityQ37282402
Chromatin insulators: regulatory mechanisms and epigenetic inheritanceQ37292727
Using DNA mechanics to predict in vitro nucleosome positions and formation energies.Q37298599
Nucleosome organization in the Drosophila genome.Q37326387
Global dynamics of proteins: bridging between structure and functionQ37700683
Normal mode analysis and applications in biological physicsQ37852957
Genome architecture: domain organization of interphase chromosomesQ38090110
Twenty-five years of nucleic acid simulationsQ39399632
A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit ElectrostaticsQ40265109
Elastic Network Models of Nucleic Acids FlexibilityQ40291898
Core promoter elements of eukaryotic genes have a highly distinctive mechanical propertyQ40404840
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomeQ41336121
Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogrammingQ41833143
Exploring polymorphisms in B-DNA helical conformations.Q42370883
Sequence-dependent DNA deformability studied using molecular dynamics simulationsQ42734623
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide compositionQ46935039
DNAlive: a tool for the physical analysis of DNA at the genomic scaleQ48074408
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue12
P407language of work or nameEnglishQ1860
P304page(s)e0143760
P577publication date2015-12-01
P1433published inPLOS OneQ564954
P1476titleSimple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence
P478volume10

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cites work (P2860)
Q60915875Coarse-Grained Protein Dynamics Studies Using Elastic Network Models
Q63246790Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures
Q59576144Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model
Q39452127Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition
Q42314768The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
Q57022615iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou's PseAAC to pseudo-tri-nucleotide composition

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