ArticleNucleic acids research2025
CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
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Authors and funding
5 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.