Farré-Gil David, Bayarri Genis, Laughton Charles A, Hospital Adam, Orozco Modesto
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.
Department of Mathematics and Computer Science, University of Barcelona, Barcelona 08007, Spain.
Nucleic Acids Res. 2025 Jul 7;53(W1):W151-W157. doi: 10.1093/nar/gkaf371.
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein-DNA segments thanks to a Langevin dynamics coarse-grained (CG) model working with a machine-learning (ML) fitted C1'-resolution Hamiltonian. The CG trajectories can be back-mapped to atomistic resolution using another ML algorithm trained on a large database of molecular dynamics (MD) simulations. The method allows the user to get structural and dynamic information on large (kilobase range) portions of both protein-bound and free DNA, to transform conceptual cartoons into structural and dynamical models. Trajectories are analyzed using an extensive set of nucleic acid-specific analysis tools, and the results are displayed using a powerful and flexible graphic interface. The web tool uses state-of-the-art technologies such as (i) Docker components orchestrated by Docker Swarm, with containers deployed on demand for computations, (ii) WebGL-programmed NGL molecular viewer and the JavaScript plotly library for interactive plots, and (iii) noSQL-MongoDB for storage. The server is accessible at https://mmb.irbbarcelona.org/CGNAW/. The web tool is free and open to all users, and there are no login requirements.
我们展示了CGeNArateWeb，这是一种用于裸DNA和蛋白质结合染色质纤维三维模拟的新型网络工具。该服务器允许用户借助基于机器学习（ML）拟合的C1'分辨率哈密顿量的朗之万动力学粗粒度（CG）模型，获得线性、环状或蛋白质-DNA片段长链的动态表示。使用在大量分子动力学（MD）模拟数据库上训练的另一种ML算法，可以将CG轨迹反向映射到原子分辨率。该方法允许用户获取蛋白质结合和游离DNA的大片段（千碱基范围）的结构和动态信息，将概念性卡通转化为结构和动力学模型。使用大量核酸特异性分析工具对轨迹进行分析，并使用强大且灵活的图形界面显示结果。该网络工具使用了诸如（i）由Docker Swarm编排的Docker组件，按需部署容器进行计算，（ii）WebGL编程的NGL分子查看器和用于交互式绘图的JavaScript plotly库，以及（iii）用于存储的NoSQL-MongoDB等先进技术。可通过https://mmb.irbbarcelona.org/CGNAW/访问该服务器。该网络工具免费向所有用户开放，无需登录。
