Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes
Fig 2
Illustration of data-generation (top half) and analysis (lower half) workflow to identify possible structures of ubiquitylated linker histone in a chromatosome.
Data was produced by MD simulations driven by an expansion scheme which selects new starting structures from sparsely populated regions of phase space. The aggregated MD data is projected into a combined low-dimensional space and clustered iteratively. Clusters (i.e. characteristic conformational states) are then fitted into different chromatosome structures using a new geometric scoring method.