Spring Model - chromatin modeling tool based on OpenMM.

Chromatin structures modeling is a rapidly developing field. Parallel to the enormous growth of available experimental data, there is a growing need of building and visualizing 3D structures of nuclei, chromosomes, chromatin domains, and single loops associated with particular genes locus. Here we present a tool for chromatin domain modeling. It is available as a webservice and standalone python script. Our tool is based on molecular mechanics. It uses OpenMM engine for building models. In this method the user has to provide contacts and will obtain a 3D structure that satisfies these contacts. Additional parameters allow controlling fibre stiffness, type of initial structure and resolution. There are also options for structure refinement and modeling in a spherical container. A user may provide contacts using beads indices, or paste interactions in genome coordinates from BEDPE file. After modeling the user is able to download the structure in Protein Data Bank (PDB) file format for further analysis. We dedicate this tool to all who are interested in chromatin structures. It is suitable for quick visualization of datasets, studying the impact of structural variants (SVs), inspecting the effects of adding and removing particular contacts, measuring features like maximum distances between certain sites (e.g.promoter-enhancer) or local density of chromatin.