{"id":"https://openalex.org/W4388486476","doi":"https://doi.org/10.1109/tkde.2023.3331005","title":"GNNGO3D: Protein Function Prediction Based on 3D Structure and Functional Hierarchy Learning","display_name":"GNNGO3D: Protein Function Prediction Based on 3D Structure and Functional Hierarchy Learning","publication_year":2023,"publication_date":"2023-11-08","ids":{"openalex":"https://openalex.org/W4388486476","doi":"https://doi.org/10.1109/tkde.2023.3331005"},"language":"en","primary_location":{"id":"doi:10.1109/tkde.2023.3331005","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2023.3331005","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Knowledge and Data Engineering","raw_type":"journal-article"},"type":"article","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/A5114098005","display_name":"Liyuan Zhang","orcid":"https://orcid.org/0000-0001-9268-9850"},"institutions":[{"id":"https://openalex.org/I4800084","display_name":"Southwest Jiaotong University","ror":"https://ror.org/00hn7w693","country_code":"CN","type":"education","lineage":["https://openalex.org/I4800084"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liyuan Zhang","raw_affiliation_strings":["School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, China","institution_ids":["https://openalex.org/I4800084"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060855407","display_name":"Yongquan Jiang","orcid":"https://orcid.org/0000-0003-1651-595X"},"institutions":[{"id":"https://openalex.org/I4800084","display_name":"Southwest Jiaotong University","ror":"https://ror.org/00hn7w693","country_code":"CN","type":"education","lineage":["https://openalex.org/I4800084"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongquan Jiang","raw_affiliation_strings":["School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, Sichuan, China","Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, Sichuan, China","institution_ids":["https://openalex.org/I4800084"]},{"raw_affiliation_string":"Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu, Sichuan, China","institution_ids":["https://openalex.org/I4800084"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068951317","display_name":"Yan Yang","orcid":"https://orcid.org/0000-0002-6134-6094"},"institutions":[{"id":"https://openalex.org/I4800084","display_name":"Southwest Jiaotong University","ror":"https://ror.org/00hn7w693","country_code":"CN","type":"education","lineage":["https://openalex.org/I4800084"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Yang","raw_affiliation_strings":["School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, Sichuan, China","Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, Sichuan, China","institution_ids":["https://openalex.org/I4800084"]},{"raw_affiliation_string":"Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu, Sichuan, China","institution_ids":["https://openalex.org/I4800084"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5114098005"],"corresponding_institution_ids":["https://openalex.org/I4800084"],"apc_list":null,"apc_paid":null,"fwci":2.0011,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.86823486,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"8","first_page":"3867","last_page":"3878"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.8802317380905151},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6889558434486389},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5607427358627319},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.48822692036628723},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.48137572407722473},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4639105200767517},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4603535830974579},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.44749024510383606},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.44048359990119934},{"id":"https://openalex.org/keywords/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.4403912425041199},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4305066764354706},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.39439502358436584},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.3259398937225342},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1777973473072052},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1139884889125824}],"concepts":[{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.8802317380905151},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6889558434486389},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5607427358627319},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.48822692036628723},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.48137572407722473},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4639105200767517},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4603535830974579},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.44749024510383606},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.44048359990119934},{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.4403912425041199},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4305066764354706},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.39439502358436584},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.3259398937225342},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1777973473072052},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1139884889125824},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","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},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tkde.2023.3331005","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2023.3331005","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Knowledge and Data Engineering","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G1786514912","display_name":null,"funder_award_id":"2682021ZTPY110","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3249808475","display_name":null,"funder_award_id":"61976247","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation 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/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":0,"referenced_works":[],"related_works":["https://openalex.org/W2470147982","https://openalex.org/W2159663778","https://openalex.org/W1789072987","https://openalex.org/W2065993463","https://openalex.org/W2034313881","https://openalex.org/W4322579338","https://openalex.org/W2181899571","https://openalex.org/W2135470984","https://openalex.org/W2082535576","https://openalex.org/W1568877569"],"abstract_inverted_index":{"Protein":[0],"sequences":[1],"accumulate":[2],"in":[3,121],"large":[4],"quantities,":[5],"and":[6,26,91,106,150,175],"the":[7,21,44,49,54,62,66,88,125,132,145],"traditional":[8],"method":[9,133,162],"of":[10,43,68,100,109,118,127,134],"annotating":[11],"protein":[12,31,50,63,69,102,110,114,136,148,155,170],"function":[13,32,111,137,171],"by":[14,138],"experiment":[15],"has":[16],"been":[17],"unable":[18],"to":[19,38,61,112,152,165],"bridge":[20],"gap":[22],"between":[23,147],"annotated":[24],"proteins":[25],"unannotated":[27],"proteins.":[28],"Machine":[29],"learning-based":[30],"prediction":[33],"is":[34,58,71,163],"an":[35],"effective":[36],"approach":[37],"solve":[39,76],"this":[40,77],"problem.":[41],"Most":[42],"existing":[45,166],"methods":[46,167],"only":[47],"use":[48],"sequence":[51,174],"but":[52],"ignore":[53],"three-dimensional":[55,89],"structure":[56,90,141],"which":[57],"closely":[59],"related":[60],"function.":[64,115,156],"And":[65],"hierarchy":[67,93],"functions":[70],"not":[72],"adequately":[73],"considered.":[74],"To":[75],"problem,":[78],"we":[79],"propose":[80],"a":[81],"graph":[82],"neural":[83],"network":[84],"(GNNGO3D)":[85],"that":[86,122,160],"combines":[87],"functional":[92,128],"learning.":[94],"GNNGO3D":[95,119],"simultaneously":[96],"uses":[97],"three":[98],"kinds":[99],"information:":[101],"sequence,":[103],"tertiary":[104,140],"structure,":[105],"hierarchical":[107],"relationship":[108,146],"predict":[113,154],"The":[116],"novelty":[117],"lies":[120],"it":[123],"integrates":[124],"learning":[126,144],"level":[129],"information":[130],"into":[131],"predicting":[135,169],"using":[139],"information,":[142],"fully":[143],"functions,":[149],"helping":[151],"better":[153],"Experimental":[157],"results":[158],"show":[159],"our":[161],"superior":[164],"for":[168],"based":[172],"on":[173],"structure.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}