{"id":"https://openalex.org/W4408943178","doi":"https://doi.org/10.1021/acs.jcim.5c00004","title":"Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization","display_name":"Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization","publication_year":2025,"publication_date":"2025-03-28","ids":{"openalex":"https://openalex.org/W4408943178","doi":"https://doi.org/10.1021/acs.jcim.5c00004","pmid":"https://pubmed.ncbi.nlm.nih.gov/40152222"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00004","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00004","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102698907","display_name":"Yaxian Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxian Cai","raw_affiliation_strings":["College of Information Engineering","Zhejiang University of Technology"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Zhejiang University of Technology","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101601745","display_name":"Ziying Zhang","orcid":"https://orcid.org/0000-0002-1521-8470"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziying Zhang","raw_affiliation_strings":["College of Information Engineering","Zhejiang University of Technology"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Zhejiang University of Technology","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058288245","display_name":"Xiangyu Xu","orcid":"https://orcid.org/0000-0003-4238-3567"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangyu Xu","raw_affiliation_strings":["College of Information Engineering","Zhejiang University of Technology"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Zhejiang University of Technology","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100741489","display_name":"Liang Xu","orcid":"https://orcid.org/0000-0002-4381-558X"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Xu","raw_affiliation_strings":["College of Information Engineering","Zhejiang University of Technology"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Zhejiang University of Technology","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069686992","display_name":"Yu Chen","orcid":"https://orcid.org/0000-0003-0622-0760"},"institutions":[{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":[],"is_corresponding":false,"raw_author_name":"Yu Chen","raw_affiliation_strings":["School of Computer Science and Technology","Soochow University"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Soochow University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049735973","display_name":"Guijun Zhang","orcid":"https://orcid.org/0000-0002-7815-5884"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guijun Zhang","raw_affiliation_strings":["College of Information Engineering","Zhejiang University of Technology"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Zhejiang University of Technology","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023785113","display_name":"Xiaogen Zhou","orcid":"https://orcid.org/0000-0001-6839-1923"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaogen Zhou","raw_affiliation_strings":["College of Information Engineering","Zhejiang University of Technology"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Zhejiang University of Technology","institution_ids":["https://openalex.org/I55712492"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5023785113","https://openalex.org/A5049735973"],"corresponding_institution_ids":["https://openalex.org/I55712492"],"apc_list":null,"apc_paid":null,"fwci":17.3653,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.98612946,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"65","issue":"7","first_page":"3800","last_page":"3811"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12762","display_name":"Crystallography and Radiation Phenomena","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.9829999804496765,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/coupling","display_name":"Coupling (piping)","score":0.6274840831756592},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5078583359718323},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5011415481567383},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4893619418144226},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3398911952972412},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3309408724308014},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3272251486778259},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15835371613502502}],"concepts":[{"id":"https://openalex.org/C131584629","wikidata":"https://www.wikidata.org/wiki/Q4308705","display_name":"Coupling (piping)","level":2,"score":0.6274840831756592},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5078583359718323},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5011415481567383},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4893619418144226},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3398911952972412},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3309408724308014},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3272251486778259},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15835371613502502},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00004","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00004","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40152222","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40152222","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1320274221","display_name":null,"funder_award_id":"2022ZD0115103","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G1500733556","display_name":null,"funder_award_id":"62201506","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2154317","display_name":null,"funder_award_id":"RF-C2024006","funder_id":"https://openalex.org/F4554350417","funder_display_name":"Fundamental Research Funds for the Provincial Universities of Zhejiang"},{"id":"https://openalex.org/G7271978295","display_name":null,"funder_award_id":"62203389","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4554350417","display_name":"Fundamental Research Funds for the Provincial Universities of Zhejiang","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1595159159","https://openalex.org/W1709194643","https://openalex.org/W1964716020","https://openalex.org/W1985145180","https://openalex.org/W2043701535","https://openalex.org/W2084283552","https://openalex.org/W2086549128","https://openalex.org/W2102245393","https://openalex.org/W2112756815","https://openalex.org/W2115540209","https://openalex.org/W2136567909","https://openalex.org/W2180441778","https://openalex.org/W2790309735","https://openalex.org/W2793039150","https://openalex.org/W2963436022","https://openalex.org/W2973457155","https://openalex.org/W3014088204","https://openalex.org/W3094051077","https://openalex.org/W3108495343","https://openalex.org/W3114526705","https://openalex.org/W3149440285","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3199186332","https://openalex.org/W4226143586","https://openalex.org/W4226302535","https://openalex.org/W4237954928","https://openalex.org/W4285393885","https://openalex.org/W4285816840","https://openalex.org/W4293475204","https://openalex.org/W4295165394","https://openalex.org/W4317952730","https://openalex.org/W4388728609","https://openalex.org/W4390952090","https://openalex.org/W4392136306","https://openalex.org/W4392155415","https://openalex.org/W4393100304","https://openalex.org/W4394819744","https://openalex.org/W4396721167","https://openalex.org/W4399916751","https://openalex.org/W4400201692","https://openalex.org/W4403609453","https://openalex.org/W4404408757"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756","https://openalex.org/W3086377361"],"abstract_inverted_index":{"With":[0],"the":[1,25,28,34,37],"breakthroughs":[2],"in":[3],"protein":[4,87],"structure":[5],"prediction":[6],"technology,":[7],"constructing":[8],"atomic":[9,64,108],"structures":[10,65,109],"from":[11],"cryo-electron":[12,80],"microscopy":[13],"(cryo-EM)":[14],"density":[15,67,111],"maps":[16,85],"through":[17],"structural":[18,59],"fitting":[19,107],"has":[20],"become":[21],"increasingly":[22],"critical.":[23],"However,":[24],"accuracy":[26],"of":[27,36,86],"constructed":[29],"models":[30],"heavily":[31],"relies":[32],"on":[33,73],"precision":[35],"structure-to-map":[38],"fitting.":[39],"In":[40],"this":[41],"study,":[42],"we":[43],"introduce":[44],"DEMO-EMfit,":[45],"a":[46,57,74],"progressive":[47],"method":[48],"that":[49,95],"integrates":[50],"deep":[51],"learning-based":[52],"backbone":[53],"map":[54],"extraction":[55],"with":[56],"global-local":[58],"pose":[60],"search":[61],"to":[62],"fit":[63],"into":[66,110],"maps.":[68,112],"DEMO-EMfit":[69,96],"was":[70],"extensively":[71],"evaluated":[72],"benchmark":[75],"data":[76],"set":[77],"comprising":[78],"both":[79],"tomography":[81],"(cryo-ET)":[82],"and":[83,88,103],"cryo-EM":[84],"nucleic":[89],"acid":[90],"complexes.":[91],"The":[92],"results":[93],"demonstrate":[94],"outperforms":[97],"state-of-the-art":[98],"approaches,":[99],"offering":[100],"an":[101],"efficient":[102],"accurate":[104],"tool":[105],"for":[106]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}