This system is a set of controls designed to represent all possible DNA sequence variants at each of the 146 dimer step locations in an octasome.
The MMTV is known to position six nucleosomes, referred to as nucleosomes A to F. Our systems were modeled by docking the relevant MMTV sequence to 1KX5.
NUC146 represents a set of simulations based on x-ray structures, 2CV5, with the mutation to the histone for different species.
The systems were built manually and represent single-point mutations associated with disruption of the SIN complex.
The first set of threading experiments conducted included nucleosomes representing the mostly highly occupied and most well defined nucleosome for each chromosome of s cerevesia denoted POS, along with nucleosomes corresponding to nucleosome free regions in chromosomes 2,4,5,8 and 16, denoted NFR.