{"id":"https://openalex.org/W4406053946","doi":"https://doi.org/10.1093/bib/bbae694","title":"GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites","display_name":"GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4406053946","doi":"https://doi.org/10.1093/bib/bbae694","pmid":"https://pubmed.ncbi.nlm.nih.gov/39749667"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae694","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae694","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae694/61321525/bbae694.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae694/61321525/bbae694.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012810423","display_name":"Shanshan Fu","orcid":"https://orcid.org/0000-0003-0307-5588"},"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":"Shanshan Fu","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100326845","display_name":"Dan Liu","orcid":"https://orcid.org/0000-0002-4704-9798"},"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":"Dan Liu","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100458160","display_name":"Chi Zhang","orcid":"https://orcid.org/0000-0002-1324-2311"},"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":"Chi 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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031334632","display_name":"Xinhe Huang","orcid":"https://orcid.org/0000-0003-4190-0737"},"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":"Xinhe Huang","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053239155","display_name":"Leming Xiao","orcid":"https://orcid.org/0000-0002-6152-492X"},"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":"Leming Xiao","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101272895","display_name":"Miaoying Zhao","orcid":"https://orcid.org/0009-0003-2890-0975"},"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":"Miaoying Zhao","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100357305","display_name":"Jiayi Zhang","orcid":"https://orcid.org/0000-0002-7334-4256"},"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":"Jiayi 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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066426246","display_name":"Qiang Xiao","orcid":"https://orcid.org/0000-0003-4691-7052"},"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":"Qiang Xiao","raw_affiliation_strings":["School of Artificial Intelligence and Automation, Huazhong University of Science and Technology , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Automation, Huazhong University of Science and Technology , Luoyu Road 1037, Wuhan, Hubei 430074 ,","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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","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":false,"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,"],"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 , Luoyu Road 1037, Wuhan, Hubei 430074 ,","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.1866,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56621446,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"26","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12104","display_name":"Protein Tyrosine Phosphatases","score":0.9983999729156494,"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/T12104","display_name":"Protein Tyrosine Phosphatases","score":0.9983999729156494,"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":0.9979000091552734,"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":0.996999979019165,"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/dephosphorylation","display_name":"Dephosphorylation","score":0.9581314325332642},{"id":"https://openalex.org/keywords/phosphatase","display_name":"Phosphatase","score":0.7865563631057739},{"id":"https://openalex.org/keywords/phosphoserine","display_name":"Phosphoserine","score":0.7073697447776794},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.6263159513473511},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5298153162002563},{"id":"https://openalex.org/keywords/kinase","display_name":"Kinase","score":0.4826646149158478},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4770721197128296},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.47418412566185},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4640480875968933},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45126038789749146},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39611563086509705},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3503638803958893}],"concepts":[{"id":"https://openalex.org/C181912034","wikidata":"https://www.wikidata.org/wiki/Q1101143","display_name":"Dephosphorylation","level":4,"score":0.9581314325332642},{"id":"https://openalex.org/C178666793","wikidata":"https://www.wikidata.org/wiki/Q422476","display_name":"Phosphatase","level":3,"score":0.7865563631057739},{"id":"https://openalex.org/C2780307904","wikidata":"https://www.wikidata.org/wiki/Q2701649","display_name":"Phosphoserine","level":4,"score":0.7073697447776794},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.6263159513473511},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5298153162002563},{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.4826646149158478},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4770721197128296},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.47418412566185},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4640480875968933},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45126038789749146},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39611563086509705},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3503638803958893},{"id":"https://openalex.org/C2776414213","wikidata":"https://www.wikidata.org/wiki/Q183290","display_name":"Serine","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","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":"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":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","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":"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae694","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae694","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae694/61321525/bbae694.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39749667","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39749667","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11695897","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11695897","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11695897/pdf/bbae694.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae694","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae694","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae694/61321525/bbae694.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"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/G6316337628","display_name":null,"funder_award_id":"2022YFC2704304","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6552285623","display_name":null,"funder_award_id":"32341021","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7381466469","display_name":null,"funder_award_id":"32341020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G798236531","display_name":null,"funder_award_id":"2021YFF0702000","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406053946.pdf"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1522484198","https://openalex.org/W1683245560","https://openalex.org/W1865966390","https://openalex.org/W1881469793","https://openalex.org/W1964504843","https://openalex.org/W1966223981","https://openalex.org/W1982903637","https://openalex.org/W2003060606","https://openalex.org/W2019848334","https://openalex.org/W2021672234","https://openalex.org/W2030205108","https://openalex.org/W2043794217","https://openalex.org/W2067598924","https://openalex.org/W2073179024","https://openalex.org/W2079009246","https://openalex.org/W2101085456","https://openalex.org/W2118151336","https://openalex.org/W2133305588","https://openalex.org/W2134079593","https://openalex.org/W2139576101","https://openalex.org/W2148126636","https://openalex.org/W2150541721","https://openalex.org/W2156407548","https://openalex.org/W2160679716","https://openalex.org/W2168642368","https://openalex.org/W2334711093","https://openalex.org/W2409039558","https://openalex.org/W2465181069","https://openalex.org/W2510568608","https://openalex.org/W2562811703","https://openalex.org/W2616887300","https://openalex.org/W2635415917","https://openalex.org/W2779836448","https://openalex.org/W2893791677","https://openalex.org/W2898909792","https://openalex.org/W2900206619","https://openalex.org/W2901496107","https://openalex.org/W2917858269","https://openalex.org/W2928662855","https://openalex.org/W2999615587","https://openalex.org/W3003774652","https://openalex.org/W3004392625","https://openalex.org/W3011515036","https://openalex.org/W3024517740","https://openalex.org/W3042756937","https://openalex.org/W3115309223","https://openalex.org/W3134163647","https://openalex.org/W3140922284","https://openalex.org/W3173216909","https://openalex.org/W4214881459","https://openalex.org/W4303456975","https://openalex.org/W4317831504","https://openalex.org/W4375954646","https://openalex.org/W4376114480","https://openalex.org/W4388233463","https://openalex.org/W4389462411","https://openalex.org/W4393947060","https://openalex.org/W4401522252"],"related_works":["https://openalex.org/W2810494566","https://openalex.org/W1966455810","https://openalex.org/W2394109710","https://openalex.org/W2400718772","https://openalex.org/W2073576842","https://openalex.org/W4248691508","https://openalex.org/W2068751031","https://openalex.org/W2061891400","https://openalex.org/W1969692562","https://openalex.org/W2054888896"],"abstract_inverted_index":{"Protein":[0],"phosphorylation":[1,37],"is":[2,204],"dynamically":[3],"and":[4,10,13,78,110,125,140,163,179,196],"reversibly":[5],"regulated":[6],"by":[7],"protein":[8,11,171],"kinases":[9],"phosphatases,":[12],"plays":[14],"an":[15],"essential":[16],"role":[17],"in":[18,173],"orchestrating":[19],"a":[20,27,49,84,130,216],"wide":[21],"range":[22],"of":[23,29,42,95,107,114,202,222],"biological":[24],"processes.":[25],"Although":[26],"number":[28],"tools":[30],"have":[31],"been":[32],"developed":[33,83],"for":[34,64,92,147,219],"predicting":[35,148],"kinase-specific":[36],"sites":[38,45,67,98],"(p-sites),":[39],"computational":[40,145],"prediction":[41,90,94,181],"phosphatase-specific":[43,96,156],"dephosphorylation":[44,66,97,150],"remains":[46],"to":[47,143],"be":[48,177,184],"great":[50],"challenge.":[51],"In":[52,152],"this":[53],"study,":[54],"we":[55,82,103],"manually":[56],"curated":[57],"4393":[58],"experimentally":[59],"identified":[60],"site-specific":[61],"phosphatase-substrate":[62],"relationships":[63],"3463":[65],"occurring":[68],"on":[69],"phosphoserine,":[70],"phosphothreonine,":[71],"and/or":[72],"phosphotyrosine":[73],"residues,":[74],"from":[75],"the":[76,88,93,180],"literature":[77],"public":[79],"databases.":[80],"Then,":[81],"hybrid":[85],"learning":[86,116,162],"framework,":[87],"group-based":[89],"system":[91],"(GPSD).":[99],"For":[100,165],"model":[101,132],"training,":[102],"integrated":[104],"10":[105],"types":[106,113],"sequence":[108],"features":[109],"utilized":[111],"three":[112],"machine":[115],"methods,":[117],"including":[118],"penalized":[119],"logistic":[120],"regression,":[121],"deep":[122],"neural":[123,127],"networks,":[124],"transformer":[126],"networks.":[128],"First,":[129],"pretrained":[131],"was":[133],"constructed":[134,159],"using":[135],"561":[136],"416":[137],"nonredundant":[138],"p-sites":[139],"then":[141],"fine-tuned":[142],"generate":[144],"models":[146],"general":[149],"sites.":[151],"addition,":[153],"103":[154],"individual":[155],"predictors":[157],"were":[158],"via":[160],"transfer":[161],"meta-learning.":[164],"site":[166],"prediction,":[167],"one":[168],"or":[169],"multiple":[170],"sequences":[172],"FASTA":[174],"format":[175],"could":[176],"inputted,":[178],"results":[182],"will":[183],"shown":[185],"together":[186],"with":[187],"additional":[188],"annotations,":[189],"such":[190],"as":[191,215],"protein-protein":[192],"interactions,":[193],"structural":[194],"information,":[195],"disorder":[197],"propensity.":[198],"The":[199],"online":[200],"service":[201],"GPSD":[203,212],"freely":[205],"available":[206],"at":[207],"https://gpsd.biocuckoo.cn/.":[208],"We":[209],"believe":[210],"that":[211],"can":[213],"serve":[214],"valuable":[217],"tool":[218],"further":[220],"analysis":[221],"dephosphorylation.":[223]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
