Training-free atomistic prediction of nucleosome occupancy (Q33674530)

28 July 2017

title

Training-free atomistic prediction of nucleosome occupancy (English)

1 reference

28 July 2017

2

Michael Levitt

1 reference

28 July 2017

Peter Minary

1

1 reference

28 July 2017

language of work or name

English

0 references

publication date

14 April 2014

1 reference

Proceedings of the National Academy of Sciences of the United States of America

28 July 2017

published in

1 reference

28 July 2017

volume

111

1 reference

28 July 2017

issue

17

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28 July 2017

page(s)

6293-6298

1 reference

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

28 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=4035975

A map of nucleosome positions in yeast at base-pair resolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

DNA methylation-associated silencing of tumor-suppressor microRNAs in cancer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Cytosine methylation alters DNA mechanical properties

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Nucleosomes protect DNA from DNA methylation in vivo and in vitro.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Chromatin higher-order structures and gene regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Prediction of nucleosome positioning based on transcription factor binding sites

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Relationship between nucleosome positioning and DNA methylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

DNA architecture, deformability, and nucleosome positioning

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

G+C content dominates intrinsic nucleosome occupancy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Linking DNA methylation and histone modification: patterns and paradigms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

The DNA-encoded nucleosome organization of a eukaryotic genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Chromatin remodeling: insights and intrigue from single-molecule studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Epigenetics: a landscape takes shape

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

DNA methylation and gene silencing in cancer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Genome-scale identification of nucleosome positions in S. cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

The structure of DNA in the nucleosome core

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Altered methylation patterns in cancer cell genomes: cause or consequence?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

14 July 2018

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=4035975

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

SGD: Saccharomyces Genome Database

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

The pitch of chromatin DNA is reflected in its nucleotide sequence

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

High sequence specificity of micrococcal nuclease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Chromatin Structure: A Repeating Unit of Histones and DNA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Sequence periodicities in chicken nucleosome core DNA.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4035975

Methods of conjugate gradients for solving linear systems

14 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1404475111

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1404475111

Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and of B-Z junctions

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24733939

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24733939

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1404475111

1 reference

28 July 2017

0 references

1 reference

28 July 2017

1 reference