CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers

Abstract

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.