Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.
Methods. 2020 Oct 1;181-182:62-69. doi: 10.1016/j.ymeth.2019.11.014. Epub 2019 Nov 30.
Chromatin structure 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 gene loci. 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 and utilizes the OpenMM engine for model generation. In this method the user provides contacts between chromatin regions and obtains a 3D structure that satisfies them. Additional parameters allow for the control of fibre stiffness, initial structure adjustments and simulation resolution, there are also options for structure refinement and modeling in a spherical container. The user may provide contacts in the form of bead indices, or insert interactions in genome coordinates sourced from BEDPE files. After the simulation is complete, the user is able to download the structure in the Protein Data Bank (PDB) 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, and measuring features such as maximum distances between sites (e.g.promoter-enhancer), or local chromatin density.
染色质结构建模是一个快速发展的领域。随着可用实验数据的大量增长，人们越来越需要构建和可视化核、染色体、染色质域和与特定基因座相关的单个环的 3D 结构。在这里，我们提供了一种用于染色质结构建模的工具；它有一个网络服务和一个独立的 Python 脚本。我们的工具基于分子力学，并利用 OpenMM 引擎进行模型生成。在这种方法中，用户提供染色质区域之间的接触，并获得满足这些接触的 3D 结构。额外的参数允许控制纤维刚度、初始结构调整和模拟分辨率，还有在球形容器中进行结构细化和建模的选项。用户可以以珠粒索引的形式提供接触，或者将交互作用插入源自 BEDPE 文件的基因组坐标中。模拟完成后，用户可以将结构以 Protein Data Bank (PDB) 格式下载，以便进一步分析。我们将这个工具献给所有对染色质结构感兴趣的人。它适用于快速可视化数据集，研究结构变体 (SV) 的影响，检查添加和删除特定接触的效果，以及测量诸如位点之间的最大距离（例如启动子-增强子）或局部染色质密度等特征。
