{"id":"https://openalex.org/W2576361275","doi":"https://doi.org/10.1109/bibm.2016.7822490","title":"Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy","display_name":"Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2576361275","doi":"https://doi.org/10.1109/bibm.2016.7822490","mag":"2576361275","pmid":"https://pubmed.ncbi.nlm.nih.gov/29770260"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822490","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822490","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5007355292","display_name":"Rongjian Li","orcid":"https://orcid.org/0000-0003-2739-5893"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rongjian Li","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529","Department of Computer Science, Old Dominion University, Norfolk, Virginia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, Virginia","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080683855","display_name":"Dong Si","orcid":"https://orcid.org/0000-0001-7039-2589"},"institutions":[{"id":"https://openalex.org/I4210138624","display_name":"University of Washington Bothell","ror":"https://ror.org/02ygzhr13","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210138624"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Si","raw_affiliation_strings":["Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA 98011","Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA 98011","institution_ids":["https://openalex.org/I4210138624"]},{"raw_affiliation_string":"Division of Computing and Software Systems, University of Washington Bothell, Bothell, WA","institution_ids":["https://openalex.org/I4210138624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063558254","display_name":"Tao Zeng","orcid":"https://orcid.org/0000-0001-8006-3287"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao Zeng","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164","School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052278550","display_name":"Shuiwang Ji","orcid":"https://orcid.org/0000-0002-4205-4563"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuiwang Ji","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164","School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049641499","display_name":"Jing He","orcid":"https://orcid.org/0000-0002-7249-4746"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing He","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529","Department of Computer Science, Old Dominion University, Norfolk, Virginia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, Virginia 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, Virginia","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":14.0165,"has_fulltext":false,"cited_by_count":70,"citation_normalized_percentile":{"value":0.98183042,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"2016","issue":null,"first_page":"41","last_page":"46"},"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":0.9988999962806702,"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":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.982699990272522,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9779000282287598,"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.8053826689720154},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7499819993972778},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6914699077606201},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.6795424222946167},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.6076747179031372},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5452365279197693},{"id":"https://openalex.org/keywords/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.5139009952545166},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.4726872742176056},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4249206483364105},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08243927359580994},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance","display_name":"Nuclear magnetic resonance","score":0.05957689881324768}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.8053826689720154},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7499819993972778},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6914699077606201},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6795424222946167},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6076747179031372},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5452365279197693},{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.5139009952545166},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.4726872742176056},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4249206483364105},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08243927359580994},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.05957689881324768}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/bibm.2016.7822490","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822490","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:29770260","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29770260","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:europepmc.org:4871971","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5952046","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"mag:2751199270","is_oa":false,"landing_page_url":"http://jglobal.jst.go.jp/en/public/20090422/201702219092254114","pdf_url":null,"source":{"id":"https://openalex.org/S4306512817","display_name":"IEEE Conference Proceedings","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"IEEE Conference Proceedings","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W22040386","https://openalex.org/W1568929544","https://openalex.org/W1849277567","https://openalex.org/W1897603052","https://openalex.org/W1903029394","https://openalex.org/W1923697677","https://openalex.org/W1966323820","https://openalex.org/W1975118489","https://openalex.org/W1983364832","https://openalex.org/W1994086483","https://openalex.org/W1995043996","https://openalex.org/W1999141286","https://openalex.org/W2018816581","https://openalex.org/W2032219149","https://openalex.org/W2037373017","https://openalex.org/W2046141572","https://openalex.org/W2053880783","https://openalex.org/W2054116168","https://openalex.org/W2076978930","https://openalex.org/W2080333910","https://openalex.org/W2082526668","https://openalex.org/W2096732301","https://openalex.org/W2097117768","https://openalex.org/W2098477387","https://openalex.org/W2134557905","https://openalex.org/W2137747821","https://openalex.org/W2147791333","https://openalex.org/W2152086886","https://openalex.org/W2155089380","https://openalex.org/W2163605009","https://openalex.org/W2169358216","https://openalex.org/W2169799657","https://openalex.org/W2169805405","https://openalex.org/W2194775991","https://openalex.org/W2233871097","https://openalex.org/W2305071738","https://openalex.org/W2395611524","https://openalex.org/W2412782625","https://openalex.org/W2963840672","https://openalex.org/W6600893292","https://openalex.org/W6640295612","https://openalex.org/W6674855086","https://openalex.org/W6684191040","https://openalex.org/W6687483927","https://openalex.org/W6696085341","https://openalex.org/W6698315864"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W4375867731","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"The":[0],"detection":[1],"of":[2,5,24,38,48,73,89,106,134,154],"secondary":[3,71,103,151],"structure":[4,104,152],"proteins":[6,107,155],"using":[7],"three":[8],"dimensional":[9],"(3D)":[10],"cryo-electron":[11],"microscopy":[12],"(cryo-EM)":[13],"images":[14,26],"is":[15,27],"still":[16],"a":[17,79],"challenging":[18],"task":[19],"when":[20],"the":[21,36,45,87,102,117,131,139,150],"spatial":[22,119],"resolution":[23,160],"cryo-EM":[25,97,158],"at":[28],"medium":[29,159],"level":[30],"(5-10\u00c5).":[31],"Prior":[32],"researches":[33],"focused":[34],"on":[35,148],"usage":[37],"local":[39],"features":[40,66],"that":[41,85,138],"may":[42],"not":[43],"capture":[44],"global":[46,65],"information":[47,120],"image":[49,98],"objects.":[50],"In":[51,75],"this":[52],"study,":[53],"we":[54,77,124],"propose":[55,125],"to":[56,61,101,126],"use":[57],"deep":[58],"learning":[59],"methods":[60],"extract":[62],"high":[63],"representative":[64],"and":[67,112],"then":[68],"automatically":[69],"detect":[70],"structures":[72],"proteins.":[74],"particular,":[76],"build":[78],"convolutional":[80,132],"neural":[81],"network":[82],"(CNN)":[83],"classifier":[84,142],"predicts":[86],"probability":[88],"label":[90],"for":[91],"every":[92],"individual":[93],"voxel":[94],"in":[95,121,130],"3D":[96,118,128,157],"with":[99],"respect":[100],"elements":[105,153],"such":[108],"as":[109],"\u03b1-helix,":[110],"\u03b2-sheet":[111],"background.":[113],"To":[114],"effectively":[115],"incorporate":[116],"protein":[122],"structures,":[123],"perform":[127],"convolutions":[129],"layers":[133],"CNNs.":[135],"We":[136],"show":[137],"proposed":[140],"CNN":[141],"can":[143],"outperform":[144],"existing":[145],"SVM":[146],"method":[147],"identifying":[149],"from":[156],"images.":[161]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":9}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
