Training-free atomistic prediction of nucleosome occupancy.

  title={Training-free atomistic prediction of nucleosome occupancy.},
  author={Peter Minary and Michael Levitt},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  volume={111 17},
Nucleosomes alter gene expression by preventing transcription factors from occupying binding sites along DNA. DNA methylation can affect nucleosome positioning and so alter gene expression epigenetically (without changing DNA sequence). Conventional methods to predict nucleosome occupancy are trained on observed DNA sequence patterns or known DNA oligonucleotide structures. They are statistical and lack the physics needed to predict subtle epigenetic changes due to DNA methylation. The training… CONTINUE READING
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Publications referenced by this paper.
Showing 1-10 of 39 references

DNA architecture, deformability, and nucleosome positioning.

Journal of biomolecular structure & dynamics • 2010
View 10 Excerpts
Highly Influenced

Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers

A Pérez
Biophys J 92(11):3817–3829 • 2007
View 3 Excerpts
Highly Influenced

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

Proceedings of the National Academy of Sciences of the United States of America • 1998
View 5 Excerpts
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