{"id":"https://openalex.org/W4317388119","doi":"https://doi.org/10.1093/bib/bbac631","title":"Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites","display_name":"Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites","publication_year":2023,"publication_date":"2023-01-18","ids":{"openalex":"https://openalex.org/W4317388119","doi":"https://doi.org/10.1093/bib/bbac631","pmid":"https://pubmed.ncbi.nlm.nih.gov/36653898"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac631","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbac631/49560395/bbac631.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/2/bbac631/49560395/bbac631.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100411464","display_name":"Xiao Wang","orcid":"https://orcid.org/0000-0002-3113-5149"},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiao Wang","raw_affiliation_strings":["School of Computer and Communication Engineering, Zhengzhou University of Light Industry , No. 136, Science Avenue, 450002, Zhengzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Engineering, Zhengzhou University of Light Industry , No. 136, Science Avenue, 450002, Zhengzhou , China","institution_ids":["https://openalex.org/I23171815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062164377","display_name":"Zhaoyuan Ding","orcid":"https://orcid.org/0000-0003-0965-2446"},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoyuan Ding","raw_affiliation_strings":["School of Computer and Communication Engineering, Zhengzhou University of Light Industry , No. 136, Science Avenue, 450002, Zhengzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Engineering, Zhengzhou University of Light Industry , No. 136, Science Avenue, 450002, Zhengzhou , China","institution_ids":["https://openalex.org/I23171815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100324870","display_name":"Rong Wang","orcid":"https://orcid.org/0000-0001-6904-806X"},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rong Wang","raw_affiliation_strings":["School of Computer and Communication Engineering, Zhengzhou University of Light Industry , No. 136, Science Avenue, 450002, Zhengzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Engineering, Zhengzhou University of Light Industry , No. 136, Science Avenue, 450002, Zhengzhou , China","institution_ids":["https://openalex.org/I23171815"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5106746347","display_name":"Xi Lin","orcid":"https://orcid.org/0000-0001-5303-1191"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xi Lin","raw_affiliation_strings":["Instiute of Artificial Intelligence, Xiamen University , No.4221, Xiang\u2019an South Road, 361000, Xiamen , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instiute of Artificial Intelligence, Xiamen University , No.4221, Xiang\u2019an South Road, 361000, Xiamen , China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100411464"],"corresponding_institution_ids":["https://openalex.org/I23171815"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":5.2472,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.96144884,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"24","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":1.0,"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":1.0,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965000152587891,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9947999715805054,"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/computer-science","display_name":"Computer science","score":0.8170439004898071},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7448334693908691},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7069226503372192},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6990341544151306},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5274068713188171},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4917609989643097},{"id":"https://openalex.org/keywords/recurrent-neural-network","display_name":"Recurrent neural network","score":0.46265512704849243},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.44044554233551025}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8170439004898071},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7448334693908691},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7069226503372192},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6990341544151306},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5274068713188171},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4917609989643097},{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.46265512704849243},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.44044554233551025},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac631","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbac631/49560395/bbac631.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36653898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36653898","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/bbac631","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac631","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbac631/49560395/bbac631.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4317388119.pdf","grobid_xml":"https://content.openalex.org/works/W4317388119.grobid-xml"},"referenced_works_count":89,"referenced_works":["https://openalex.org/W1591801644","https://openalex.org/W1977927254","https://openalex.org/W2049349724","https://openalex.org/W2088511656","https://openalex.org/W2102461176","https://openalex.org/W2141818629","https://openalex.org/W2147863530","https://openalex.org/W2158714788","https://openalex.org/W2280263325","https://openalex.org/W2294567968","https://openalex.org/W2345051977","https://openalex.org/W2569463473","https://openalex.org/W2765268259","https://openalex.org/W2767496117","https://openalex.org/W2768705872","https://openalex.org/W2788462335","https://openalex.org/W2797330243","https://openalex.org/W2798044596","https://openalex.org/W2808746931","https://openalex.org/W2883402437","https://openalex.org/W2885195348","https://openalex.org/W2886279431","https://openalex.org/W2888353590","https://openalex.org/W2896457183","https://openalex.org/W2908663744","https://openalex.org/W2914454976","https://openalex.org/W2938901647","https://openalex.org/W2940438782","https://openalex.org/W2943978521","https://openalex.org/W2948863695","https://openalex.org/W2949342052","https://openalex.org/W2954633061","https://openalex.org/W2962949934","https://openalex.org/W2971769670","https://openalex.org/W2982562461","https://openalex.org/W2988184648","https://openalex.org/W2995514860","https://openalex.org/W2998238598","https://openalex.org/W2999309192","https://openalex.org/W3004623993","https://openalex.org/W3024503287","https://openalex.org/W3038215960","https://openalex.org/W3047670845","https://openalex.org/W3048357930","https://openalex.org/W3082862577","https://openalex.org/W3094312164","https://openalex.org/W3096296947","https://openalex.org/W3096437212","https://openalex.org/W3116967090","https://openalex.org/W3117371146","https://openalex.org/W3136918052","https://openalex.org/W3147794567","https://openalex.org/W3159102674","https://openalex.org/W3171942304","https://openalex.org/W3172051228","https://openalex.org/W3172422681","https://openalex.org/W3177500196","https://openalex.org/W3182795819","https://openalex.org/W3185245858","https://openalex.org/W3188469295","https://openalex.org/W3193542455","https://openalex.org/W3193614607","https://openalex.org/W3199417536","https://openalex.org/W3199970975","https://openalex.org/W4210810268","https://openalex.org/W4224311147","https://openalex.org/W4225891318","https://openalex.org/W4281480754","https://openalex.org/W4281557145","https://openalex.org/W4290989027","https://openalex.org/W4297782913","https://openalex.org/W6635446068","https://openalex.org/W6689873356","https://openalex.org/W6694401350","https://openalex.org/W6696879442","https://openalex.org/W6704695948","https://openalex.org/W6731351805","https://openalex.org/W6755207826","https://openalex.org/W6759119076","https://openalex.org/W6760506965","https://openalex.org/W6763984457","https://openalex.org/W6770427332","https://openalex.org/W6772435762","https://openalex.org/W6781602502","https://openalex.org/W6796714436","https://openalex.org/W6797355663","https://openalex.org/W6798586241","https://openalex.org/W6799419190","https://openalex.org/W6810272519"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W2381570729","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W3008584592","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"Lysine":[0],"glutarylation":[1,27,50],"(Kglu)":[2],"is":[3,36,152],"a":[4],"newly":[5],"discovered":[6],"post-translational":[7],"modification":[8],"of":[9,49,53,74,138],"proteins":[10],"with":[11],"important":[12],"roles":[13],"in":[14],"mitochondrial":[15],"functions,":[16],"oxidative":[17],"damage,":[18],"etc.":[19],"The":[20,119,188],"established":[21],"biological":[22],"experimental":[23],"methods":[24,43,57],"to":[25,40,62,114,154],"identify":[26],"sites":[28],"are":[29,123,193],"often":[30],"time-consuming":[31],"and":[32,46,67,99,110,133,144,161,173,191],"costly.":[33],"Therefore,":[34],"there":[35],"an":[37,89],"urgent":[38],"need":[39],"develop":[41,88],"computational":[42,56],"for":[44],"efficient":[45],"accurate":[47],"identification":[48],"sites.":[51,118],"Most":[52],"the":[54,64,71,75,81,106,126,134,149,157,162,167,185],"existing":[55],"only":[58],"utilize":[59],"handcrafted":[60,112,135,163],"features":[61,109,113,122,136,143,160,164],"construct":[63],"prediction":[65,82],"model":[66,79,130],"do":[68],"not":[69],"consider":[70],"positive":[72],"impact":[73],"pre-trained":[76,127],"protein":[77,128],"language":[78,129],"on":[80,85],"performance.":[83],"Based":[84],"this,":[86],"we":[87],"ensemble":[90],"deep-learning":[91],"predictor":[92],"Deepro-Glu":[93,178],"that":[94,177],"combines":[95],"convolutional":[96],"neural":[97],"network":[98,104],"bidirectional":[100],"long":[101],"short-term":[102],"memory":[103],"using":[105],"deep":[107,120,158],"learning":[108,121,159,166],"traditional":[111],"predict":[115],"lysine":[116],"glutaryation":[117],"generated":[124],"from":[125],"called":[131],"ProtBert,":[132],"consist":[137],"sequence-based":[139],"features,":[140],"physicochemical":[141],"property-based":[142],"evolution":[145],"information-based":[146],"features.":[147],"Furthermore,":[148],"attention":[150,169],"mechanism":[151],"used":[153],"efficiently":[155],"integrate":[156],"by":[165],"appropriate":[168],"weights.":[170],"10-fold":[171],"cross-validation":[172],"independent":[174],"tests":[175],"demonstrate":[176],"achieves":[179],"competitive":[180],"or":[181],"superior":[182],"performance":[183],"than":[184],"state-of-the-art":[186],"methods.":[187],"source":[189],"codes":[190],"data":[192],"publicly":[194],"available":[195],"at":[196],"https://github.com/xwanggroup/Deepro-Glu.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
