TMB-iBIOMES: An iBIOMES-Lite Database of Nucleosome Trajectories and Meta-Analysis

Here we introduce our TMB-iBIOMES database which serves as both a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES-Lite as a tool for managing a laboratory's simulation inventory. TMB-iBIOMES contains over 20 microseconds of all atom molecular dynamics simulations for over 500 different realizations of the nucleosome. For every simulation, the original input, output, de-watered trajectories, RMSD, and DNA helical parameter data are provided. Closely related simulations are grouped together, and a meta-analysis of each group is provided. The data can be navigated in a file browser format or downloaded directly with command line tools. Collectively the simulations provide a novel view of nucleosomal DNA. Compared to DNA free in solution, DNA on the nucleosome is not highly deformed or tightly restricted as determined by DNA helical parameter analysis. The overall conformation is restricted to a specific left-handed super helix, but the range of conformations explored by individual base pairs is larger than that observed for DNA free in solution.