Multiscale Molecular Modelling of Chromatin with MultiMM: From Nucleosomes to the Whole Genome

Abstract

MotivationWe present a user-friendly 3D chromatin simulation model based on OpenMM, addressing the challenges posed by existing models with use-specific implementations. Our approach employs a multi-scale energy minimization strategy, capturing chromatins hierarchical structure. Initiating with a Hilbert curve-based structure, users can input files specifying nucleosome positioning, loops, compartments, or subcompartments. ResultsThe model utilizes an energy minimization approach with a large choice of numerical integrators, providing the entire genomes structure within minutes. Output files include the generated structures for each chromosome, offering a versatile and accessible tool for chromatin simulation in bioinformatics studies. Furthermore, MultiMM is capable of producing nucleosomeresolution structures by making simplistic geometric assumptions about the structure and the density of nucleosomes on the DNA. Code availabilityOpen-source software and the manual are freely available on https://github.com/SFGLab/MultiMM.