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https://hdl.handle.net/2445/221841
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DC Field | Value | Language |
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dc.contributor.author | Farré Gil, David | - |
dc.contributor.author | Arcon, Juan Pablo | - |
dc.contributor.author | Laughton, Charles A. | - |
dc.contributor.author | Orozco López, Modesto | - |
dc.date.accessioned | 2025-06-27T13:15:45Z | - |
dc.date.available | 2025-06-27T13:15:45Z | - |
dc.date.issued | 2024-07-08 | - |
dc.identifier.issn | 0305-1048 | - |
dc.identifier.uri | https://hdl.handle.net/2445/221841 | - |
dc.description.abstract | We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. The method is sequence-dependent and reproduces very well not only local, but also global physical properties of DNA. The efficiency of the method allows us to recover with a reduced computational effort high-quality atomic-resolution ensembles of segments containing many kilobases of DNA, entering into the gene range or even the entire DNA of certain cellular organelles. | - |
dc.format.extent | 11 p. | - |
dc.format.mimetype | application/pdf | - |
dc.language.iso | eng | - |
dc.publisher | Oxford University Press | - |
dc.relation.isformatof | Reproducció del document publicat a: https://doi.org/10.1093/nar/gkae444 | - |
dc.relation.ispartof | Nucleic Acids Research, 2024, vol. 52, num.12, p. 6791-6801 | - |
dc.relation.uri | https://doi.org/10.1093/nar/gkae444 | - |
dc.rights | cc-by-nc (c) Farré-Gil, D. et al., 2024 | - |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | * |
dc.source | Articles publicats en revistes (Bioquímica i Biomedicina Molecular) | - |
dc.subject.classification | Biotecnologia | - |
dc.subject.classification | Sistemes hamiltonians | - |
dc.subject.classification | Dinàmica molecular | - |
dc.subject.classification | Cromatina | - |
dc.subject.other | Biotechnology | - |
dc.subject.other | Hamiltonian systems | - |
dc.subject.other | Molecular dynamics | - |
dc.subject.other | Chromatin | - |
dc.title | CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes | - |
dc.type | info:eu-repo/semantics/article | - |
dc.type | info:eu-repo/semantics/publishedVersion | - |
dc.identifier.idgrec | 758977 | - |
dc.date.updated | 2025-06-27T13:15:45Z | - |
dc.rights.accessRights | info:eu-repo/semantics/openAccess | - |
Appears in Collections: | Articles publicats en revistes (Bioquímica i Biomedicina Molecular) Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona)) |
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895471.pdf | 8.69 MB | Adobe PDF | View/Open |
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