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gkaf371.pdf (5.67 MB)

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2025-05-10

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cc-by-nc (c) Farré Gil, David et al., 2025
Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/221185

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

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Recurs relacionat

https://doi.org/10.1093/nar/gkaf371

Resum

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.

Matèries

Computational biology, Cromatina, Servidors web

Matèries (anglès)

Biologia computacional, Chromatin

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Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))

Citació

FARRÉ GIL, David, et al. CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers. Nucleic Acids Research. 2025. Vol. 53, num. W1, pags. W151–W157. ISSN 1362-4962. [consulted: 27 of June of 2026]. Available at: https://hdl.handle.net/2445/221185

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