Workflow Optimization for Comparative Molecular Dynamics of Mono-Nucleosomes

Thomas Bishop, Louisiana Tech University

Usage Details

Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. Given that a nucleosome contains 147 base pairs of DNA described with a four letter code (A,C,G,T) there are over 4¹⁴⁷ ~ 10⁸⁸, realizations of the nucleosome. An exhaustive study by any means is not possible. However, informatics analysis of next generation sequencing data allows researchers to hone in on epigenetic markers spanning a few base pairs of an individual's genome. Understanding epigenetic mechanisms requires sequence based informatics be coupled with bio-physical-chemical based material studies. We will enable such understanding by coupling comparative molecular dynamics studies of nucleosomes with traditional informatics analysis of any sequence of interest. For this reason our goal is to develop tools for on-demand, comparative all-atom molecular dynamics studies of ensembles of nucleosomes constructed with arbitrary DNA sequences.