{"id":"https://openalex.org/W4399411203","doi":"https://doi.org/10.1109/tcbb.2024.3410350","title":"RGCNPPIS: A Residual Graph Convolutional Network for Protein-Protein Interaction Site Prediction","display_name":"RGCNPPIS: A Residual Graph Convolutional Network for Protein-Protein Interaction Site Prediction","publication_year":2024,"publication_date":"2024-06-06","ids":{"openalex":"https://openalex.org/W4399411203","doi":"https://doi.org/10.1109/tcbb.2024.3410350","pmid":"https://pubmed.ncbi.nlm.nih.gov/38843057"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3410350","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3410350","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5053729346","display_name":"Jian Zhong","orcid":"https://orcid.org/0009-0007-0010-3949"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jian Zhong","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061114972","display_name":"Haochen Zhao","orcid":"https://orcid.org/0000-0001-8794-3148"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haochen Zhao","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001452497","display_name":"Qichang Zhao","orcid":"https://orcid.org/0000-0002-8319-9793"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qichang Zhao","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060126743","display_name":"Ruikang Zhou","orcid":"https://orcid.org/0009-0000-9363-9134"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruikang Zhou","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001547268","display_name":"Lishen Zhang","orcid":"https://orcid.org/0000-0002-1704-9551"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lishen Zhang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100702161","display_name":"Fei Guo","orcid":"https://orcid.org/0000-0001-8346-0798"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Guo","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5053729346"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":null,"apc_paid":null,"fwci":4.0555,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.94623242,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"6","first_page":"1676","last_page":"1684"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9968000054359436,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9968000054359436,"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":0.9886999726295471,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9851999878883362,"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/residual","display_name":"Residual","score":0.7387537360191345},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5897101163864136},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5696090459823608},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34073901176452637},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.24975624680519104},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.17376485466957092}],"concepts":[{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.7387537360191345},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5897101163864136},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5696090459823608},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34073901176452637},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.24975624680519104},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.17376485466957092}],"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3410350","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3410350","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38843057","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38843057","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3194490278","display_name":null,"funder_award_id":"2022JJ30750","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G8324054742","display_name":null,"funder_award_id":"62332020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8450505776","display_name":null,"funder_award_id":"62072473","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/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1483099488","https://openalex.org/W2009672036","https://openalex.org/W2009815491","https://openalex.org/W2012852001","https://openalex.org/W2017230497","https://openalex.org/W2031918459","https://openalex.org/W2043699100","https://openalex.org/W2051210555","https://openalex.org/W2055043387","https://openalex.org/W2084619201","https://openalex.org/W2096119514","https://openalex.org/W2103485392","https://openalex.org/W2141627824","https://openalex.org/W2151412657","https://openalex.org/W2155194485","https://openalex.org/W2166814967","https://openalex.org/W2211387173","https://openalex.org/W2280888683","https://openalex.org/W2570083522","https://openalex.org/W2612935389","https://openalex.org/W2754800853","https://openalex.org/W2772865572","https://openalex.org/W2806884808","https://openalex.org/W2907063321","https://openalex.org/W2944679105","https://openalex.org/W2955690154","https://openalex.org/W2964051675","https://openalex.org/W2971405760","https://openalex.org/W2990045899","https://openalex.org/W2992752586","https://openalex.org/W3013976849","https://openalex.org/W3080498684","https://openalex.org/W3164046276","https://openalex.org/W3197696221","https://openalex.org/W4229031603","https://openalex.org/W4309438076","https://openalex.org/W4317369987","https://openalex.org/W4386317415","https://openalex.org/W6696048330","https://openalex.org/W6738964360","https://openalex.org/W6779961489"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2560215812","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2949601986","https://openalex.org/W2001405890","https://openalex.org/W4300237897"],"abstract_inverted_index":{"Accurate":[0],"identification":[1],"of":[2,13,91,159],"protein-protein":[3],"interaction":[4],"(PPI)":[5],"sites":[6],"is":[7,95,168],"crucial":[8],"for":[9,52,103,172],"understanding":[10],"the":[11,36,66,76,89,96,117,125,139,157],"mechanisms":[12],"biological":[14],"processes,":[15],"developing":[16],"PPI":[17,54,104,173],"networks,":[18],"and":[19,33,74,124,137,162],"detecting":[20],"protein":[21],"functions.":[22],"Currently,":[23],"most":[24],"computational":[25],"methods":[26,149],"primarily":[27],"concentrate":[28],"on":[29,150],"sequence":[30],"context":[31],"features":[32,69,83,102],"rarely":[34],"consider":[35],"spatial":[37,72,86],"neighborhood":[38],"features.":[39],"To":[40,88],"address":[41],"this":[42,94],"limitation,":[43],"we":[44,59],"propose":[45,109],"a":[46,61],"novel":[47],"residual":[48,112],"graph":[49,113],"convolutional":[50],"network":[51],"structure-based":[53],"site":[55,105,174],"prediction":[56],"(RGCNPPIS).":[57],"Specifically,":[58],"use":[60],"GCN":[62,127],"module":[63,78],"to":[64,79,115],"extract":[65,80],"global":[67],"structural":[68,82,101,122],"from":[70,84],"all":[71],"neighborhoods,":[73],"utilize":[75],"GraphSage":[77],"local":[81,85,100,121],"neighborhoods.":[87],"best":[90],"our":[92],"knowledge,":[93],"first":[97],"work":[98],"utilizing":[99],"prediction.":[106,175],"We":[107],"also":[108],"an":[110,169],"enhanced":[111],"connection":[114],"combine":[116],"initial":[118],"node":[119,129],"representation,":[120,130],"features,":[123],"previous":[126],"layer's":[128],"which":[131],"enables":[132],"information":[133],"transfer":[134],"between":[135],"layers":[136],"alleviates":[138],"over-smoothing":[140],"problem.":[141],"Evaluation":[142],"results":[143,158],"demonstrate":[144],"that":[145,166],"RGCNPPIS":[146,167],"outperforms":[147],"state-of-the-art":[148],"three":[151],"independent":[152],"test":[153],"sets.":[154],"In":[155],"addition,":[156],"ablation":[160],"experiments":[161],"case":[163],"studies":[164],"confirm":[165],"effective":[170],"tool":[171]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
