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

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)...

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Autores: Farré Gil, David, Bayarri Sarda, Genis, Laughton, Charles A., Hospital Gasch, Adam, Orozco López, Modesto
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/221185
Acceso en línea:https://hdl.handle.net/2445/221185
Access Level:acceso abierto
Palabra clave:Computational biology
Cromatina
Servidors web
Biologia computacional
Chromatin
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spelling CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibersFarré Gil, DavidBayarri Sarda, GenisLaughton, Charles A.Hospital Gasch, AdamOrozco López, ModestoComputational biologyCromatinaServidors webBiologia computacionalChromatinWe 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.Oxford University Press2025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/221185Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.1093/nar/gkaf371Nucleic Acids Research, 2025https://doi.org/10.1093/nar/gkaf371cc-by-nc (c) Farré Gil, David et al., 2025http://creativecommons.org/licenses/by-nc/3.0/es/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/2211852026-05-27T06:46:51Z
dc.title.none.fl_str_mv CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
title CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
spellingShingle CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
Farré Gil, David
Computational biology
Cromatina
Servidors web
Biologia computacional
Chromatin
title_short CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
title_full CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
title_fullStr CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
title_full_unstemmed CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
title_sort CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers
dc.creator.none.fl_str_mv Farré Gil, David
Bayarri Sarda, Genis
Laughton, Charles A.
Hospital Gasch, Adam
Orozco López, Modesto
author Farré Gil, David
author_facet Farré Gil, David
Bayarri Sarda, Genis
Laughton, Charles A.
Hospital Gasch, Adam
Orozco López, Modesto
author_role author
author2 Bayarri Sarda, Genis
Laughton, Charles A.
Hospital Gasch, Adam
Orozco López, Modesto
author2_role author
author
author
author
dc.subject.none.fl_str_mv Computational biology
Cromatina
Servidors web
Biologia computacional
Chromatin
topic Computational biology
Cromatina
Servidors web
Biologia computacional
Chromatin
description 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.
publishDate 2025
dc.date.none.fl_str_mv 2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/221185
url https://hdl.handle.net/2445/221185
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1093/nar/gkaf371
Nucleic Acids Research, 2025
https://doi.org/10.1093/nar/gkaf371
dc.rights.none.fl_str_mv cc-by-nc (c) Farré Gil, David et al., 2025
http://creativecommons.org/licenses/by-nc/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by-nc (c) Farré Gil, David et al., 2025
http://creativecommons.org/licenses/by-nc/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812455

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