{"doi":"10.1107/s2059798324006776","title":"Likelihood-based interactive local docking into cryo-EM maps in <i>ChimeraX</i>","abstract":"The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.","journal":"Acta Crystallographica Section D Structural Biology","year":2024,"id":442924,"datarank":0.3941656057703281,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.06458191916989513,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.06458191916989513,"corpus_percentile":null,"corpus_rank":null,"citation_count":8,"citer_count":8,"citers_with_citation_signal":4,"citers_with_endowment":4,"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":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":30000,"name":"Eric F. Pettersen","orcid":null,"position":1,"is_corresponding":false},{"id":6674,"name":"Airlie J. McCoy","orcid":"0009-0001-6855-9631","position":2,"is_corresponding":false},{"id":103425,"name":"Tristan I. Croll","orcid":"0000-0002-3514-8377","position":3,"is_corresponding":false},{"id":59243,"name":"Thomas C. Terwilliger","orcid":"0000-0001-6384-0320","position":4,"is_corresponding":false},{"id":364587,"name":"Billy K. Poon","orcid":"0000-0001-9633-6067","position":5,"is_corresponding":false},{"id":30005,"name":"Elaine C. Meng","orcid":null,"position":6,"is_corresponding":false},{"id":364586,"name":"Dorothée Liebschner","orcid":"0000-0003-3921-3209","position":7,"is_corresponding":false},{"id":39882,"name":"Paul D. Adams","orcid":"0000-0001-9333-8219","position":8,"is_corresponding":false},{"id":6667,"name":"Randy J. Read","orcid":"0000-0001-8273-0047","position":0,"is_corresponding":true}],"reference_count":25,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:01:20.107161Z","pmid":"39058381","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":[]}