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Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/221841
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes
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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.
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FARRÉ GIL, David, et al. CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes. Nucleic Acids Research. 2024. Vol. 52, num. 12, pags. 6791-6801. ISSN 0305-1048. [consulted: 15 of August of 2026]. Available at: https://hdl.handle.net/2445/221841