{"id":"https://openalex.org/W3099816816","doi":"https://doi.org/10.1186/s12859-020-3504-z","title":"DeepFrag-k: a fragment-based deep learning approach for protein fold recognition","display_name":"DeepFrag-k: a fragment-based deep learning approach for protein fold recognition","publication_year":2020,"publication_date":"2020-11-01","ids":{"openalex":"https://openalex.org/W3099816816","doi":"https://doi.org/10.1186/s12859-020-3504-z","mag":"3099816816","pmid":"https://pubmed.ncbi.nlm.nih.gov/33203392"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3504-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3504-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3504-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3504-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021847688","display_name":"Wessam Elhefnawy","orcid":null},"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":"Wessam Elhefnawy","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, U.S.A"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, U.S.A","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Li","raw_affiliation_strings":["Department of Computer Science, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["Department of Computer Science, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079316675","display_name":"Yaohang Li","orcid":"https://orcid.org/0000-0003-0178-1876"},"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":true,"raw_author_name":"Yaohang Li","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, U.S.A.. yaohang@cs.odu.edu","Department of Computer Science, Old Dominion University, Norfolk, U.S.A"],"raw_orcid":"https://orcid.org/0000-0003-0178-1876","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, U.S.A.. yaohang@cs.odu.edu","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, U.S.A","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079316675"],"corresponding_institution_ids":["https://openalex.org/I81365321"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2790},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2790},"fwci":0.5964,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.64387854,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"21","issue":"S6","first_page":"203","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.4083999991416931,"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"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.4083999991416931,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.4059000015258789,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.03999999910593033,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.8035768270492554},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.7775017023086548},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.730888843536377},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.7083085179328918},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6995232701301575},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.6442062854766846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6176317930221558},{"id":"https://openalex.org/keywords/fold","display_name":"Fold (higher-order function)","score":0.5402190089225769},{"id":"https://openalex.org/keywords/deep-belief-network","display_name":"Deep belief network","score":0.42288050055503845},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37432020902633667},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19167658686637878},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1509815752506256}],"concepts":[{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.8035768270492554},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.7775017023086548},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.730888843536377},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7083085179328918},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6995232701301575},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6442062854766846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6176317930221558},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.5402190089225769},{"id":"https://openalex.org/C97385483","wikidata":"https://www.wikidata.org/wiki/Q16954980","display_name":"Deep belief network","level":3,"score":0.42288050055503845},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37432020902633667},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19167658686637878},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1509815752506256},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-3504-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3504-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3504-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33203392","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33203392","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:digitalcommons.odu.edu:computerscience_fac_pubs-1179","is_oa":true,"landing_page_url":"https://digitalcommons.odu.edu/computerscience_fac_pubs/177","pdf_url":"https://digitalcommons.odu.edu/cgi/viewcontent.cgi?article=1179&context=computerscience_fac_pubs","source":{"id":"https://openalex.org/S4377196314","display_name":"ODU Digital Commons (Old Dominion University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I81365321","host_organization_name":"Old Dominion University","host_organization_lineage":["https://openalex.org/I81365321"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science Faculty Publications","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:dfc87560e51b4809a35405ac794dd9df","is_oa":true,"landing_page_url":"https://doaj.org/article/dfc87560e51b4809a35405ac794dd9df","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss S6, Pp 1-12 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7672895","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7672895","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-3504-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3504-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-3504-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7799999713897705}],"awards":[{"id":"https://openalex.org/G3328780670","display_name":null,"funder_award_id":"61728211","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4043378463","display_name":null,"funder_award_id":"61832019","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3099816816.pdf","grobid_xml":"https://content.openalex.org/works/W3099816816.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W154472438","https://openalex.org/W391985582","https://openalex.org/W591482569","https://openalex.org/W1487894924","https://openalex.org/W1541024235","https://openalex.org/W1971784866","https://openalex.org/W2009638021","https://openalex.org/W2022368654","https://openalex.org/W2027550567","https://openalex.org/W2038210560","https://openalex.org/W2038681300","https://openalex.org/W2047672715","https://openalex.org/W2050587358","https://openalex.org/W2051583813","https://openalex.org/W2061391250","https://openalex.org/W2085277871","https://openalex.org/W2091169672","https://openalex.org/W2095131443","https://openalex.org/W2106030336","https://openalex.org/W2108067237","https://openalex.org/W2119331235","https://openalex.org/W2147462290","https://openalex.org/W2150661553","https://openalex.org/W2151180344","https://openalex.org/W2158714788","https://openalex.org/W2191134648","https://openalex.org/W2192419461","https://openalex.org/W2279853298","https://openalex.org/W2311607323","https://openalex.org/W2398543370","https://openalex.org/W2514866683","https://openalex.org/W2540069603","https://openalex.org/W2619851495","https://openalex.org/W2747370968","https://openalex.org/W2912478095","https://openalex.org/W6638553918"],"related_works":["https://openalex.org/W1973480752","https://openalex.org/W2805502594","https://openalex.org/W2965546495","https://openalex.org/W4389116644","https://openalex.org/W1181095405","https://openalex.org/W2153315159","https://openalex.org/W4253208712","https://openalex.org/W3103844505","https://openalex.org/W259157601","https://openalex.org/W2594876342"],"abstract_inverted_index":{"BACKGROUND:":[0],"One":[1],"of":[2,38,45,129],"the":[3,36,48,60,74,86,90,104],"most":[4,106],"essential":[5],"problems":[6],"in":[7,102,146],"structural":[8,62,135],"bioinformatics":[9],"is":[10,43,126,148],"protein":[11,39,121,140,160],"fold":[12,28,40,122,161],"recognition.":[13,41,123,162],"In":[14],"this":[15],"paper,":[16],"we":[17],"design":[18],"a":[19,52,65,69,78,127],"novel":[20],"deep":[21,79,143],"learning":[22,144],"architecture,":[23],"so-called":[24],"DeepFrag-k,":[25],"which":[26,109],"identifies":[27],"discriminative":[29,115],"features":[30,157],"at":[31],"fragment":[32,70,87,116],"level":[33],"to":[34,58,84,113,119,150,158],"improve":[35,120,159],"accuracy":[37,101],"DeepFrag-k":[42,98,147],"composed":[44],"two":[46],"stages:":[47],"first":[49],"stage":[50,76],"employs":[51],"multi-modal":[53],"Deep":[54],"Belief":[55],"Network":[56],"(DBN)":[57],"predict":[59],"potential":[61],"fragments":[63,130,154],"given":[64],"sequence,":[66],"represented":[67],"as":[68,134,155],"vector,":[71],"and":[72],"then":[73],"second":[75],"uses":[77],"convolutional":[80],"neural":[81],"network":[82],"(CNN)":[83],"classify":[85],"vector":[88],"into":[89],"corresponding":[91],"fold.":[92],"RESULTS:":[93],"Our":[94],"results":[95],"show":[96],"that":[97,131],"yields":[99],"92.98%":[100],"predicting":[103],"top-100":[105],"popular":[107],"fragments,":[108],"can":[110,132],"be":[111],"used":[112],"generate":[114],"feature":[117],"vectors":[118],"CONCLUSIONS:":[124],"There":[125],"set":[128],"serve":[133],"\"keywords\"":[136],"distinguishing":[137],"between":[138],"major":[139],"folds.":[141],"The":[142],"architecture":[145],"able":[149],"accurately":[151],"identify":[152],"these":[153],"structure":[156]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
