{"id":"https://openalex.org/W4390992233","doi":"https://doi.org/10.1109/bibm58861.2023.10385619","title":"Deep-USIpred: identifying substrates of ubiquitin protein ligases E3 and deubiquitinases with pretrained protein embedding and bayesian neural network","display_name":"Deep-USIpred: identifying substrates of ubiquitin protein ligases E3 and deubiquitinases with pretrained protein embedding and bayesian neural network","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992233","doi":"https://doi.org/10.1109/bibm58861.2023.10385619"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385619","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5025137072","display_name":"Jia Wang","orcid":"https://orcid.org/0000-0003-2308-2259"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia Wang","raw_affiliation_strings":["Shenzhen University,College of Computer Science and Software Engineering,Shenzhen,China","College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen University,College of Computer Science and Software Engineering,Shenzhen,China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063005114","display_name":"Gui-Qing Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gui-Qing Pan","raw_affiliation_strings":["Shenzhen University,College of Computer Science and Software Engineering,Shenzhen,China","College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen University,College of Computer Science and Software Engineering,Shenzhen,China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100393871","display_name":"Jianqiang Li","orcid":"https://orcid.org/0000-0002-2208-962X"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian-Qiang Li","raw_affiliation_strings":["Shenzhen University,College of Computer Science and Software Engineering,Shenzhen,China","College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen University,College of Computer Science and Software Engineering,Shenzhen,China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I4210137009","display_name":"Shaanxi Polytechnic Institute","ror":"https://ror.org/03c8jqn92","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210137009"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xue-Qun Shang","raw_affiliation_strings":["Northwesterm Polytechnical University,School of Computer Science,Shaanxi,China","School of Computer Science, Northwesterm Polytechnical University, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwesterm Polytechnical University,School of Computer Science,Shaanxi,China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I4210137009"]},{"raw_affiliation_string":"School of Computer Science, Northwesterm Polytechnical University, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019805735","display_name":"Zhu\u2010Hong You","orcid":"https://orcid.org/0000-0003-1266-2696"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I4210137009","display_name":"Shaanxi Polytechnic Institute","ror":"https://ror.org/03c8jqn92","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210137009"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhu-Hong You","raw_affiliation_strings":["Northwesterm Polytechnical University,School of Computer Science,Shaanxi,China","School of Computer Science, Northwesterm Polytechnical University, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwesterm Polytechnical University,School of Computer Science,Shaanxi,China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I4210137009"]},{"raw_affiliation_string":"School of Computer Science, Northwesterm Polytechnical University, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017713277","display_name":"Yu\u2010An Huang","orcid":"https://orcid.org/0000-0002-5346-2394"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I4210137009","display_name":"Shaanxi Polytechnic Institute","ror":"https://ror.org/03c8jqn92","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210137009"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu-An Huang","raw_affiliation_strings":["Northwesterm Polytechnical University,School of Computer Science,Shaanxi,China","School of Computer Science, Northwesterm Polytechnical University, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwesterm Polytechnical University,School of Computer Science,Shaanxi,China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I4210137009"]},{"raw_affiliation_string":"School of Computer Science, Northwesterm Polytechnical University, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"32","issue":null,"first_page":"2277","last_page":"2280"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9994000196456909,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9994000196456909,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9933000206947327,"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":0.9923999905586243,"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/deep-learning","display_name":"Deep learning","score":0.7404444217681885},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6869915723800659},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6671677827835083},{"id":"https://openalex.org/keywords/ubiquitin-ligase","display_name":"Ubiquitin ligase","score":0.6480716466903687},{"id":"https://openalex.org/keywords/ubiquitin","display_name":"Ubiquitin","score":0.5972991585731506},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5378607511520386},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49323123693466187},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.4846780598163605},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.4730488359928131},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4596438407897949},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.42101937532424927},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3659670352935791},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3162667751312256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19632825255393982},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08131682872772217},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06802484393119812}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7404444217681885},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6869915723800659},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6671677827835083},{"id":"https://openalex.org/C134459356","wikidata":"https://www.wikidata.org/wiki/Q4274835","display_name":"Ubiquitin ligase","level":4,"score":0.6480716466903687},{"id":"https://openalex.org/C25602115","wikidata":"https://www.wikidata.org/wiki/Q407111","display_name":"Ubiquitin","level":3,"score":0.5972991585731506},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5378607511520386},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49323123693466187},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.4846780598163605},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.4730488359928131},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4596438407897949},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.42101937532424927},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3659670352935791},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3162667751312256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19632825255393982},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08131682872772217},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06802484393119812},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385619","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1976041483","https://openalex.org/W2008044453","https://openalex.org/W2064221650","https://openalex.org/W2100547839","https://openalex.org/W2131950257","https://openalex.org/W2944951456","https://openalex.org/W2951433247","https://openalex.org/W2995514860","https://openalex.org/W3146944767","https://openalex.org/W3205926919","https://openalex.org/W4317233339","https://openalex.org/W6617145748","https://openalex.org/W6763868836"],"related_works":["https://openalex.org/W1970861248","https://openalex.org/W2102368462","https://openalex.org/W2054919679","https://openalex.org/W2016556888","https://openalex.org/W3110810129","https://openalex.org/W2007249806","https://openalex.org/W3195663446","https://openalex.org/W4396676821","https://openalex.org/W2032459623","https://openalex.org/W2040788846"],"abstract_inverted_index":{"Identifying":[0],"the":[1,13,97,100,119,133,140],"substrates":[2],"of":[3,15,24,99,121,135],"ubiquitin":[4],"protein":[5,70,77],"ligase":[6],"(E3)":[7],"and":[8,29,44,47,83,106,123,152],"deubiquitinases":[9],"(DUB)":[10],"contributes":[11],"to":[12,89,142],"discovery":[14,145],"potential":[16,141],"therapeutic":[17],"targets":[18],"for":[19,34,132,146],"diseases.":[20,148],"However,":[21],"experimental":[22,108],"identification":[23],"E3/DUB-substrate":[25,36,67,136],"interactions":[26,37,68],"is":[27],"costly":[28],"time-consuming.":[30],"Current":[31],"computational":[32],"methods":[33],"predicting":[35],"rely":[38],"heavily":[39],"on":[40,103,118],"specific":[41],"domain":[42],"knowledge":[43],"involve":[45],"complex":[46],"diverse":[48],"biological":[49],"data":[50],"processing.":[51],"To":[52],"address":[53],"this":[54],"challenge,":[55],"we":[56],"proposed":[57,73,101,126],"a":[58,80,91,129],"deep":[59,86],"learning":[60,87],"prediction":[61,93,116,134],"model,":[62],"named":[63],"Deep-USIpred,":[64],"which":[65,138],"predicts":[66],"using":[69],"sequences.":[71],"The":[72,149],"Deep-USIpred":[74],"model":[75,82,102],"encodes":[76],"sequences":[78],"with":[79],"pretrained":[81],"utilizes":[84],"1DCNN-BNN":[85],"algorithm":[88],"make":[90],"robust":[92],"model.":[94],"We":[95],"evaluated":[96],"performance":[98,117],"real":[104],"datasets,":[105],"our":[107],"results":[109],"show":[110],"that":[111],"it":[112],"can":[113],"achieve":[114],"excellent":[115],"tasks":[120],"ESI":[122],"DSI.":[124],"Our":[125],"method":[127],"provides":[128],"promising":[130],"alternative":[131],"interactions,":[137],"has":[139],"accelerate":[143],"drug":[144],"various":[147],"source":[150],"code":[151],"dataset":[153],"are":[154],"available":[155],"at":[156],"https://github.com/PGTSING/Deep-USIpred.":[157]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
