Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles

Alexey K Shaytan; Grigoriy A Armeev; Alexander Goncearenco; Victor B Zhurkin; David Landsman; Anna R Panchenko

doi:10.1016/j.dib.2016.04.073

Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles

Data Brief. 2016 May 6:7:1678-81. doi: 10.1016/j.dib.2016.04.073. eCollection 2016 Jun.

Authors

Alexey K Shaytan¹, Grigoriy A Armeev², Alexander Goncearenco³, Victor B Zhurkin⁴, David Landsman³, Anna R Panchenko³

Affiliations

¹ National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, United States; Biology Department, Lomonosov Moscow State University, Moscow 119991, Russia.
² Biology Department, Lomonosov Moscow State University, Moscow 119991, Russia.
³ National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, United States.
⁴ Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, United States.

Abstract

We present here raw trajectories of molecular dynamics simulations for nucleosome with linker DNA strands as well as minimalistic nucleosome core particle model. The simulations were done in explicit solvent using CHARMM36 force field. We used this data in the research article Shaytan et al., 2016 [1]. The trajectory files are supplemented by TCL scripts providing advanced visualization capabilities.

Keywords: Histone; Histone tails; Linker DNA; Molecular dynamics; Nucleosome.