{"id":"https://openalex.org/W4205742853","doi":"https://doi.org/10.1093/bib/bbab574","title":"GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites","display_name":"GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites","publication_year":2021,"publication_date":"2021-12-16","ids":{"openalex":"https://openalex.org/W4205742853","doi":"https://doi.org/10.1093/bib/bbab574","pmid":"https://pubmed.ncbi.nlm.nih.gov/35037020"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab574","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab574","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100704321","display_name":"Chenwei Wang","orcid":"https://orcid.org/0000-0002-0920-8639"},"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":"Chenwei Wang","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103194983","display_name":"Xiaodan Tan","orcid":null},"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":"Xiaodan Tan","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031603642","display_name":"Dachao Tang","orcid":"https://orcid.org/0000-0001-7780-454X"},"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":"Dachao Tang","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046910965","display_name":"Yujie Gou","orcid":"https://orcid.org/0000-0002-5399-9757"},"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":"Yujie Gou","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Cheng Han","orcid":null},"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":"Cheng Han","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078920713","display_name":"Wanshan Ning","orcid":"https://orcid.org/0000-0002-1410-7891"},"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":"Wanshan Ning","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-1410-7891","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008488027","display_name":"Shaofeng Lin","orcid":"https://orcid.org/0000-0002-1177-5480"},"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":"Shaofeng Lin","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-1177-5480","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043782446","display_name":"Weizhi Zhang","orcid":"https://orcid.org/0000-0002-9131-3234"},"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":"Weizhi Zhang","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-9131-3234","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100700410","display_name":"Miaomiao Chen","orcid":"https://orcid.org/0000-0002-4866-8072"},"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":"Miaomiao Chen","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019144745","display_name":"Di Peng","orcid":"https://orcid.org/0000-0002-1249-3741"},"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":"Di Peng","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-1249-3741","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052691524","display_name":"Yu Xue","orcid":"https://orcid.org/0000-0002-9403-6869"},"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":"Yu Xue","raw_affiliation_strings":["Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-9403-6869","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5052691524"],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.3617,"has_fulltext":false,"cited_by_count":65,"citation_normalized_percentile":{"value":0.89859788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"23","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9995999932289124,"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":0.9995999932289124,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9993000030517578,"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":0.9984999895095825,"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/global-positioning-system","display_name":"Global Positioning System","score":0.6926192045211792},{"id":"https://openalex.org/keywords/ubiquitin","display_name":"Ubiquitin","score":0.6589080095291138},{"id":"https://openalex.org/keywords/lysine","display_name":"Lysine","score":0.6069824695587158},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5418059229850769},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43169042468070984},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4064236283302307},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2586970925331116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2563824951648712},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23889267444610596},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.07823428511619568},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0777585506439209},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.05867007374763489}],"concepts":[{"id":"https://openalex.org/C60229501","wikidata":"https://www.wikidata.org/wiki/Q18822","display_name":"Global Positioning System","level":2,"score":0.6926192045211792},{"id":"https://openalex.org/C25602115","wikidata":"https://www.wikidata.org/wiki/Q407111","display_name":"Ubiquitin","level":3,"score":0.6589080095291138},{"id":"https://openalex.org/C2776016237","wikidata":"https://www.wikidata.org/wiki/Q178430","display_name":"Lysine","level":3,"score":0.6069824695587158},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5418059229850769},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43169042468070984},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4064236283302307},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2586970925331116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2563824951648712},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23889267444610596},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.07823428511619568},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0777585506439209},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.05867007374763489}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab574","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab574","pdf_url":null,"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:35037020","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35037020","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1063086538","display_name":null,"funder_award_id":"31970633","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1965089080","display_name":null,"funder_award_id":"2019\u00a0T120648","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G2479366607","display_name":"\u663c\u591c\u8282\u5f8b\u78f7\u9178\u5316\u53c2\u4e0e\u5b63\u8282\u6027\u60c5\u7eea\u8c03\u8282\u7684\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76","funder_award_id":"31930021","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4941527208","display_name":null,"funder_award_id":"2018\u00a0M642816","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G8129075375","display_name":null,"funder_award_id":"2019kfyRCPY043","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8407181","display_name":null,"funder_award_id":"2020\u00a0M682395","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":76,"referenced_works":["https://openalex.org/W1568400197","https://openalex.org/W1617606969","https://openalex.org/W1976041483","https://openalex.org/W1979880724","https://openalex.org/W1984148780","https://openalex.org/W1986235349","https://openalex.org/W1990453950","https://openalex.org/W1995989434","https://openalex.org/W1999212541","https://openalex.org/W2003204068","https://openalex.org/W2006505144","https://openalex.org/W2008044453","https://openalex.org/W2024543003","https://openalex.org/W2034611055","https://openalex.org/W2053502852","https://openalex.org/W2064639714","https://openalex.org/W2086831875","https://openalex.org/W2087732089","https://openalex.org/W2100547839","https://openalex.org/W2101894686","https://openalex.org/W2102554713","https://openalex.org/W2103785600","https://openalex.org/W2108984616","https://openalex.org/W2118151336","https://openalex.org/W2124052876","https://openalex.org/W2140182533","https://openalex.org/W2145786566","https://openalex.org/W2152084880","https://openalex.org/W2152339342","https://openalex.org/W2156822612","https://openalex.org/W2159675211","https://openalex.org/W2170747616","https://openalex.org/W2230399809","https://openalex.org/W2258401599","https://openalex.org/W2344751993","https://openalex.org/W2553689505","https://openalex.org/W2556028929","https://openalex.org/W2569814361","https://openalex.org/W2580091136","https://openalex.org/W2607940843","https://openalex.org/W2610582292","https://openalex.org/W2745944099","https://openalex.org/W2767152811","https://openalex.org/W2767580150","https://openalex.org/W2795989238","https://openalex.org/W2805367049","https://openalex.org/W2805520299","https://openalex.org/W2891111520","https://openalex.org/W2893791677","https://openalex.org/W2894836881","https://openalex.org/W2901879913","https://openalex.org/W2913126315","https://openalex.org/W2919709896","https://openalex.org/W2924903005","https://openalex.org/W2944951456","https://openalex.org/W2980163931","https://openalex.org/W2988906435","https://openalex.org/W3011725683","https://openalex.org/W3014226969","https://openalex.org/W3020440546","https://openalex.org/W3025651178","https://openalex.org/W3048343681","https://openalex.org/W3082590494","https://openalex.org/W3091108742","https://openalex.org/W3126854872","https://openalex.org/W3141691617","https://openalex.org/W3156007823","https://openalex.org/W3162917661","https://openalex.org/W3167998654","https://openalex.org/W3205926919","https://openalex.org/W3209420441","https://openalex.org/W4210757594","https://openalex.org/W4256202460","https://openalex.org/W6684205576","https://openalex.org/W6802256993","https://openalex.org/W6803490545"],"related_works":["https://openalex.org/W2412924645","https://openalex.org/W1968047324","https://openalex.org/W2069291669","https://openalex.org/W3162200841","https://openalex.org/W2321548162","https://openalex.org/W2586280620","https://openalex.org/W2805505483","https://openalex.org/W2334071950","https://openalex.org/W2974695603","https://openalex.org/W4317388196"],"abstract_inverted_index":{"As":[0],"an":[1,152],"important":[2],"post-translational":[3],"modification,":[4],"lysine":[5],"ubiquitination":[6,23,33,42,61,77,107,191],"participates":[7],"in":[8,15,144,173],"numerous":[9,32],"biological":[10],"processes":[11],"and":[12,75,115,132,172,206],"is":[13,24,44,210],"involved":[14],"human":[16,189],"diseases,":[17],"whereas":[18],"the":[19,53,57,71,80,141],"site":[20],"specificity":[21],"of":[22,40,59,73,113,123,157,188],"mainly":[25],"decided":[26],"by":[27],"ubiquitin-protein":[28],"ligases":[29],"(E3s).":[30],"Although":[31],"predictors":[34,178],"have":[35],"been":[36],"developed,":[37],"computational":[38],"prediction":[39,58,72,187],"E3-specific":[41,76,170,177],"sites":[43],"still":[45],"a":[46,66,147,185],"great":[47],"challenge.":[48],"Here,":[49],"we":[50,64,82,109,183],"carefully":[51],"reviewed":[52],"existing":[54,139],"tools":[55],"for":[56,70,164,197,212],"general":[60,74,106,142],"sites.":[62,78],"Also,":[63],"developed":[65],"tool":[67],"named":[68],"GPS-Uber":[69,145,201],"From":[79],"literature,":[81],"manually":[83],"collected":[84],"1311":[85],"experimentally":[86],"identified":[87],"site-specific":[88],"E3-substrate":[89],"relations,":[90],"which":[91,193],"were":[92,179],"classified":[93],"into":[94],"different":[95,102],"clusters":[96],"based":[97],"on":[98],"corresponding":[99],"E3s":[100],"at":[101,215],"levels.":[103],"To":[104],"predict":[105],"sites,":[108],"integrated":[110],"10":[111],"types":[112,122],"sequence":[114],"structure":[116],"features,":[117],"as":[118,120],"well":[119],"three":[121],"algorithms":[124],"including":[125],"penalized":[126],"logistic":[127],"regression,":[128],"deep":[129],"neural":[130,134],"network":[131],"convolutional":[133],"network.":[135],"Compared":[136],"with":[137,151],"other":[138],"tools,":[140],"model":[143],"exhibited":[146],"highly":[148],"competitive":[149],"accuracy,":[150],"area":[153],"under":[154],"curve":[155],"values":[156],"0.7649.":[158],"Then,":[159],"transfer":[160],"learning":[161],"was":[162],"adopted":[163],"each":[165],"E3":[166],"cluster":[167],"to":[168],"construct":[169],"models,":[171],"total":[174],"112":[175],"individual":[176],"implemented.":[180],"Using":[181],"GPS-Uber,":[182],"conducted":[184],"systematic":[186],"cancer-associated":[190],"events,":[192],"could":[194],"be":[195,203],"helpful":[196],"further":[198],"experimental":[199],"consideration.":[200],"will":[202],"regularly":[204],"updated,":[205],"its":[207],"online":[208],"service":[209],"free":[211],"academic":[213],"research":[214],"http://gpsuber.biocuckoo.cn/.":[216]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":24},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
