{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Posani E"],"funding":["NIGMS NIH HHS"],"pagination":["4549"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12084557"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["16(1)"],"pubmed_abstract":["The advent of single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution imaging of large macromolecules, enhancing functional insights. However, current cryo-EM refinement tools condense all single-particle images into a single structure, which can misrepresent highly flexible molecules like RNAs. Here, we combine molecular dynamics simulations with cryo-EM density maps to better account for the structural dynamics of a complex and biologically relevant RNA macromolecule. Namely, using metainference, a Bayesian method, we reconstruct an ensemble of structures of the group II intron ribozyme, which better matches experimental data, and we reveal inaccuracies of single-structure approaches in modeling flexible regions. An analysis of all RNA-containing struct"],"journal":["Nature communications"],"pubmed_title":["Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations."],"pmcid":["PMC12084557"],"funding_grant_id":["R35 GM141706"],"pubmed_authors":["Bussi G","Bonomi M","Posani E","Magistrato A","Haack D","Toor N","Janos P"],"additional_accession":[]},"is_claimable":false,"name":"Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.","description":"The advent of single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution imaging of large macromolecules, enhancing functional insights. However, current cryo-EM refinement tools condense all single-particle images into a single structure, which can misrepresent highly flexible molecules like RNAs. Here, we combine molecular dynamics simulations with cryo-EM density maps to better account for the structural dynamics of a complex and biologically relevant RNA macromolecule. Namely, using metainference, a Bayesian method, we reconstruct an ensemble of structures of the group II intron ribozyme, which better matches experimental data, and we reveal inaccuracies of single-structure approaches in modeling flexible regions. An analysis of all RNA-containing struct","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 May","modification":"2026-04-08T19:53:35.022Z","creation":"2026-04-08T14:32:01.903Z"},"accession":"S-EPMC12084557","cross_references":{"pubmed":["40379699"],"doi":["10.1038/s41467-025-59769-0"]}}