{"id":"https://openalex.org/W4393100304","doi":"https://doi.org/10.1093/bib/bbae113","title":"DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting","display_name":"DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4393100304","doi":"https://doi.org/10.1093/bib/bbae113","pmid":"https://pubmed.ncbi.nlm.nih.gov/38517699"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae113","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae113","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae113/57011708/bbae113.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae113/57011708/bbae113.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101601747","display_name":"Ziying Zhang","orcid":"https://orcid.org/0000-0002-7402-7893"},"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 , Hangzhou 310023 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","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 , Hangzhou 310023 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100363708","display_name":"Biao Zhang","orcid":"https://orcid.org/0000-0001-6097-1878"},"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":"Biao Zhang","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100693002","display_name":"Wei Zheng","orcid":"https://orcid.org/0000-0002-2984-9003"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Zheng","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109 , USA"],"raw_orcid":"https://orcid.org/0000-0002-2984-9003","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031996829","display_name":"Lydia Freddolino","orcid":"https://orcid.org/0000-0002-5821-4226"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lydia Freddolino","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109 , USA"],"raw_orcid":"https://orcid.org/0000-0002-5821-4226","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI 48109 , USA","institution_ids":["https://openalex.org/I27837315"]}]},{"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 , Hangzhou 310023 , China"],"raw_orcid":"https://orcid.org/0000-0002-7815-5884","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China","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 , Hangzhou 310023 , China"],"raw_orcid":"https://orcid.org/0000-0001-6839-1923","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023 , China","institution_ids":["https://openalex.org/I55712492"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5023785113","https://openalex.org/A5031996829","https://openalex.org/A5049735973"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I55712492"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":8.7737,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.97234144,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"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":0.9994999766349792,"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":0.9994999766349792,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9894999861717224,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular 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"}}],"keywords":[{"id":"https://openalex.org/keywords/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.8883016705513},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6738162040710449},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.6307404041290283},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.49823665618896484},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.49065080285072327},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4265936017036438},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3243246376514435},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.18051022291183472},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11620879173278809},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance","display_name":"Nuclear magnetic resonance","score":0.06549468636512756}],"concepts":[{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.8883016705513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6738162040710449},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6307404041290283},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.49823665618896484},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.49065080285072327},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4265936017036438},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3243246376514435},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.18051022291183472},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11620879173278809},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.06549468636512756},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"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":"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":"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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},{"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},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbae113","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae113","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae113/57011708/bbae113.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38517699","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38517699","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbae113","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae113","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae113/57011708/bbae113.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"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/G2313673879","display_name":null,"funder_award_id":"ACI1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4509968318","display_name":null,"funder_award_id":"R01 AI134678","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4569877226","display_name":null,"funder_award_id":"2022ZD0115103","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"},{"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/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4393100304.pdf"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1595159159","https://openalex.org/W1964716020","https://openalex.org/W1988200737","https://openalex.org/W2043701535","https://openalex.org/W2072973641","https://openalex.org/W2086549128","https://openalex.org/W2095036253","https://openalex.org/W2115540209","https://openalex.org/W2124026197","https://openalex.org/W2132629607","https://openalex.org/W2141918346","https://openalex.org/W2143815085","https://openalex.org/W2154714625","https://openalex.org/W2161151688","https://openalex.org/W2180229411","https://openalex.org/W2180441778","https://openalex.org/W2325521056","https://openalex.org/W2793039150","https://openalex.org/W2944535254","https://openalex.org/W2963436022","https://openalex.org/W2966489898","https://openalex.org/W2970515102","https://openalex.org/W2973457155","https://openalex.org/W3014088204","https://openalex.org/W3094051077","https://openalex.org/W3114526705","https://openalex.org/W3118856226","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3194187547","https://openalex.org/W4210598838","https://openalex.org/W4210926296","https://openalex.org/W4226302535","https://openalex.org/W4285393885","https://openalex.org/W4285816840","https://openalex.org/W4293475204","https://openalex.org/W4295165394","https://openalex.org/W4300105875","https://openalex.org/W4376663831","https://openalex.org/W4386979830","https://openalex.org/W4392155415","https://openalex.org/W6852139227","https://openalex.org/W6906651746"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2053286651","https://openalex.org/W1988881631","https://openalex.org/W4312462505","https://openalex.org/W1838872057","https://openalex.org/W2181743346","https://openalex.org/W2277205612","https://openalex.org/W2187401768","https://openalex.org/W2181413294"],"abstract_inverted_index":{"The":[0,71,101],"breakthrough":[1],"in":[2],"cryo-electron":[3,78],"microscopy":[4],"(cryo-EM)":[5],"technology":[6],"has":[7],"led":[8],"to":[9,41],"an":[10,44,56,91,104],"increasing":[11],"number":[12],"of":[13,16,94,98,114],"density":[14],"maps":[15,28,54,81],"biological":[17],"macromolecules.":[18],"However,":[19],"constructing":[20,48],"accurate":[21],"protein":[22,49],"complex":[23,50],"atomic":[24],"structures":[25],"from":[26,52],"cryo-EM":[27,53,116],"remains":[29],"a":[30],"challenge.":[31],"In":[32],"this":[33],"study,":[34],"we":[35],"extend":[36],"our":[37],"previously":[38],"developed":[39],"DEMO-EM":[40],"present":[42],"DEMO-EM2,":[43],"automated":[45],"method":[46,72,106],"for":[47,67],"models":[51,89],"through":[55],"iterative":[57],"assembly":[58],"procedure":[59],"intertwining":[60],"chain-":[61],"and":[62,65,82,111],"domain-level":[63],"matching":[64],"fitting":[66],"predicted":[68],"chain":[69],"models.":[70],"was":[73],"carefully":[74],"evaluated":[75],"on":[76],"27":[77],"tomography":[79],"(cryo-ET)":[80],"16":[83],"single-particle":[84],"EM":[85],"maps,":[86],"where":[87],"DEMO-EM2":[88],"achieved":[90],"average":[92],"TM-score":[93],"0.92,":[95],"outperforming":[96],"those":[97],"state-of-the-art":[99],"methods.":[100],"results":[102],"demonstrate":[103],"efficient":[105],"that":[107],"enables":[108],"the":[109],"rapid":[110],"reliable":[112],"solution":[113],"challenging":[115],"structure":[117],"modeling":[118],"problems.":[119]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":4}],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2025-10-10T00:00:00"}
