{"id":"https://openalex.org/W3163185840","doi":"https://doi.org/10.1093/bioinformatics/btab357","title":"Full-length <i>de novo</i> protein structure determination from cryo-EM maps using deep learning","display_name":"Full-length <i>de novo</i> protein structure determination from cryo-EM maps using deep learning","publication_year":2021,"publication_date":"2021-05-08","ids":{"openalex":"https://openalex.org/W3163185840","doi":"https://doi.org/10.1093/bioinformatics/btab357","mag":"3163185840","pmid":"https://pubmed.ncbi.nlm.nih.gov/33978686"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab357","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab357","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5059824731","display_name":"Jiahua He","orcid":"https://orcid.org/0000-0002-9075-4978"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahua He","raw_affiliation_strings":["School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053305024","display_name":"Sheng\u2010You Huang","orcid":"https://orcid.org/0000-0002-4209-4565"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sheng-You Huang","raw_affiliation_strings":["School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-4209-4565","affiliations":[{"raw_affiliation_string":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053305024"],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.2364,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.92233417,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"37","issue":"20","first_page":"3480","last_page":"3490"},"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":0.9904999732971191,"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":0.9904999732971191,"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":0.00279999990016222,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"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/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.6227013468742371},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5680718421936035},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4989943504333496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4948245882987976},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40694600343704224},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2795643210411072},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.1001090407371521}],"concepts":[{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.6227013468742371},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5680718421936035},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4989943504333496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4948245882987976},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40694600343704224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2795643210411072},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.1001090407371521}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab357","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab357","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33978686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33978686","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3310655903","display_name":null,"funder_award_id":"62072199","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7618829171","display_name":"\u86cb\u767d\u8d28\u76f8\u4e92\u4f5c\u7528\u7684\u591a\u4f53\u5173\u8054\u6548\u5e94\u548c\u5206\u5b50\u67d4\u6027\u7814\u7a76","funder_award_id":"31670724","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/F4320321883","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W2028843689","https://openalex.org/W2040940915","https://openalex.org/W2048875539","https://openalex.org/W2084283552","https://openalex.org/W2087064593","https://openalex.org/W2096732301","https://openalex.org/W2100455255","https://openalex.org/W2102245393","https://openalex.org/W2104130324","https://openalex.org/W2104234755","https://openalex.org/W2118233996","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2133179696","https://openalex.org/W2149360962","https://openalex.org/W2156469184","https://openalex.org/W2161072217","https://openalex.org/W2167338363","https://openalex.org/W2170747616","https://openalex.org/W2180229411","https://openalex.org/W2212589734","https://openalex.org/W2259134357","https://openalex.org/W2288234278","https://openalex.org/W2506310782","https://openalex.org/W2569402566","https://openalex.org/W2580555377","https://openalex.org/W2587625522","https://openalex.org/W2606766264","https://openalex.org/W2638004687","https://openalex.org/W2771437888","https://openalex.org/W2786390877","https://openalex.org/W2791670278","https://openalex.org/W2802061004","https://openalex.org/W2803510301","https://openalex.org/W2810204237","https://openalex.org/W2889085087","https://openalex.org/W2889917226","https://openalex.org/W2892035330","https://openalex.org/W2897504342","https://openalex.org/W2912476907","https://openalex.org/W2965789171","https://openalex.org/W2966489898","https://openalex.org/W2977933365","https://openalex.org/W2979414277","https://openalex.org/W2990714798","https://openalex.org/W2996952348","https://openalex.org/W3004081347","https://openalex.org/W3005016287","https://openalex.org/W3006253911","https://openalex.org/W3008066294","https://openalex.org/W3010499032","https://openalex.org/W3011088659","https://openalex.org/W3012316881","https://openalex.org/W3028390093","https://openalex.org/W3047785505","https://openalex.org/W3114526705","https://openalex.org/W3127623024","https://openalex.org/W3159533105","https://openalex.org/W4210352507"],"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":{"MOTIVATION:":[0],"Advances":[1],"in":[2,121,188,195],"microscopy":[3,17],"instruments":[4],"and":[5,35,54,106,115,142,167,175,193,207],"image":[6],"processing":[7],"algorithms":[8,171],"have":[9],"led":[10],"to":[11],"an":[12,48,153],"increasing":[13,49],"number":[14],"of":[15,42,62,159,190,210],"Cryo-electron":[16],"(cryo-EM)":[18],"maps.":[19],"However,":[20],"building":[21,196],"accurate":[22],"models":[23,94],"for":[24],"the":[25,39,52,104,122,205],"EM":[26,44,67,123],"maps":[27,53,68,97,137,145,162],"at":[28,98,138,146,163,222],"3-5":[29],"\u00c5":[30,140,148,165],"resolution":[31,141,149],"remains":[32],"a":[33,75,83,182],"challenging":[34],"time-consuming":[36],"process.":[37],"With":[38],"rapid":[40],"growth":[41],"deposited":[43],"maps,":[45],"there":[46],"is":[47,69],"gap":[50],"between":[51],"reconstructed/modeled":[55],"three-dimensional":[56],"(3D)":[57],"structures.":[58],"Therefore,":[59],"automatic":[60],"reconstruction":[61],"atomic-accuracy":[63,92],"full-atom":[64],"structures":[65,199],"from":[66,95],"pressingly":[70],"needed.":[71],"RESULTS:":[72],"We":[73],"present":[74],"semi-automatic":[76],"de":[77],"novo":[78],"structure":[79,117],"determination":[80],"method":[81],"using":[82,125],"deep":[84],"learning-based":[85],"framework,":[86],"named":[87],"as":[88,109,111,150,152],"DeepMM,":[89],"which":[90],"builds":[91],"all-atom":[93],"cryo-EM":[96],"near-atomic":[99],"resolution.":[100],"In":[101],"our":[102,178],"method,":[103],"main-chain":[105],"C\u03b1":[107],"positions":[108],"well":[110,151],"their":[112],"amino":[113],"acid":[114],"secondary":[116],"types":[118],"are":[119,220],"predicted":[120],"map":[124],"Densely":[126],"Connected":[127],"Convolutional":[128],"Networks.":[129],"DeepMM":[130,179],"was":[131],"extensively":[132],"validated":[133],"on":[134,200],"40":[135],"simulated":[136],"5":[139],"30":[143],"experimental":[144,161],"2.6-4.8":[147],"Electron":[154],"Microscopy":[155],"Data":[156],"Bank-wide":[157],"dataset":[158],"2931":[160],"2.6-4.9":[164],"resolution,":[166],"compared":[168],"with":[169],"state-of-the-art":[170],"including":[172],"RosettaES,":[173],"MAINMAST":[174],"Phenix.":[176],"Overall,":[177],"algorithm":[180],"obtained":[181],"significant":[183],"improvement":[184],"over":[185],"existing":[186],"methods":[187],"terms":[189],"both":[191],"accuracy":[192],"coverage":[194],"full-length":[197],"protein":[198],"all":[201],"test":[202],"sets,":[203],"demonstrating":[204],"efficacy":[206],"general":[208],"applicability":[209],"DeepMM.":[211],"AVAILABILITY":[212],"AND":[213],"IMPLEMENTATION:":[214],"http://huanglab.phys.hust.edu.cn/DeepMM.":[215],"SUPPLEMENTARY":[216],"INFORMATION:":[217],"Supplementary":[218],"data":[219],"available":[221],"Bioinformatics":[223],"online.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2021-05-24T00:00:00"}