{"doi":"10.1042/bst20240784","title":"Advancing structure modeling from cryo-EM maps with deep learning","abstract":"Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of biomolecular structures that are challenging to resolve using conventional methods. Interpreting a cryo-EM map requires accurate modeling of the structures of underlying biomolecules. Here, we concisely discuss the evolution and current state of automatic structure modeling from cryo-EM density maps. We classify modeling methods into two categories: de novo modeling methods from high-resolution maps (better than 5 Å) and methods that model by fitting individual structures of component proteins to maps at lower resolution (worse than 5 Å). Special attention is given to the role of deep learning in the modeling process, highlighting how AI-driven approaches are transformative in cryo-EM structure modeling. We conclude by discussing future directions in the field.","journal":"Biochemical Society Transactions","year":2025,"id":513194,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9475,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":558774,"name":"Genki Terashi","orcid":"0000-0002-5339-909X","position":1,"is_corresponding":false},{"id":1168386,"name":"Zicong Zhang","orcid":"0000-0002-9545-2944","position":2,"is_corresponding":false},{"id":316939,"name":"Daisuke Kihara","orcid":"0000-0003-4091-6614","position":3,"is_corresponding":false},{"id":1374225,"name":"Shu Li","orcid":"0000-0003-4667-6164","position":0,"is_corresponding":true}],"reference_count":41,"raw_metadata":null,"created_at":"2026-07-19T02:48:17.908238Z","pmid":"39927816","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}