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oai:recercat.cat:2445/2218412025-12-04T21:15:49Zcom_2072_1057col_2072_478781col_2072_478908col_2072_478917

CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes Farré Gil, David Arcon, Juan Pablo Laughton, Charles A. Orozco López, Modesto Biotecnologia Sistemes hamiltonians Dinàmica molecular Cromatina Biotechnology Hamiltonian systems Molecular dynamics Chromatin 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. 2025-06-27T13:15:45Z 2025-06-27T13:15:45Z 2024-07-08 2025-06-27T13:15:45Z info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 0305-1048 https://hdl.handle.net/2445/221841 758977 eng Reproducció del document publicat a: https://doi.org/10.1093/nar/gkae444 Nucleic Acids Research, 2024, vol. 52, num.12, p. 6791-6801 https://doi.org/10.1093/nar/gkae444 cc-by-nc (c) Farré-Gil, D. et al., 2024 https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess 11 p. application/pdf Oxford University Press Articles publicats en revistes (Bioquímica i Biomedicina Molecular)