{"id":"https://openalex.org/W4309362167","doi":"https://doi.org/10.1021/acs.jcim.2c01092","title":"RGN: Residue-Based Graph Attention and Convolutional Network for Protein\u2013Protein Interaction Site Prediction","display_name":"RGN: Residue-Based Graph Attention and Convolutional Network for Protein\u2013Protein Interaction Site Prediction","publication_year":2022,"publication_date":"2022-11-18","ids":{"openalex":"https://openalex.org/W4309362167","doi":"https://doi.org/10.1021/acs.jcim.2c01092","pmid":"https://pubmed.ncbi.nlm.nih.gov/36398714"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01092","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01092","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5100375568","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0002-1693-6888"},"institutions":[{"id":"https://openalex.org/I204553293","display_name":"China University of Petroleum, Beijing","ror":"https://ror.org/041qf4r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I204553293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum, QingDao266580, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum, QingDao266580, China","institution_ids":["https://openalex.org/I204553293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038591788","display_name":"Wenqi Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I204553293","display_name":"China University of Petroleum, Beijing","ror":"https://ror.org/041qf4r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I204553293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenqi Chen","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum, QingDao266580, China"],"raw_orcid":"https://orcid.org/0000-0002-2350-4987","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum, QingDao266580, China","institution_ids":["https://openalex.org/I204553293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028526301","display_name":"Peifu Han","orcid":"https://orcid.org/0000-0003-2818-3040"},"institutions":[{"id":"https://openalex.org/I204553293","display_name":"China University of Petroleum, Beijing","ror":"https://ror.org/041qf4r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I204553293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peifu Han","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum, QingDao266580, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum, QingDao266580, China","institution_ids":["https://openalex.org/I204553293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100372201","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-4515-6792"},"institutions":[{"id":"https://openalex.org/I204553293","display_name":"China University of Petroleum, Beijing","ror":"https://ror.org/041qf4r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I204553293"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xue Li","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum, QingDao266580, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum, QingDao266580, China","institution_ids":["https://openalex.org/I204553293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006420025","display_name":"Tao Song","orcid":"https://orcid.org/0000-0002-0130-3340"},"institutions":[{"id":"https://openalex.org/I204553293","display_name":"China University of Petroleum, Beijing","ror":"https://ror.org/041qf4r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I204553293"]},{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["CN","ES"],"is_corresponding":true,"raw_author_name":"Tao Song","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum, QingDao266580, China","Department of Artificial Intelligence, Faculty of Computer Science, Polytechnical University of Madrid, Madrid28031, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum, QingDao266580, China","institution_ids":["https://openalex.org/I204553293"]},{"raw_affiliation_string":"Department of Artificial Intelligence, Faculty of Computer Science, Polytechnical University of Madrid, Madrid28031, Spain","institution_ids":["https://openalex.org/I88060688"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5006420025"],"corresponding_institution_ids":["https://openalex.org/I204553293","https://openalex.org/I88060688"],"apc_list":null,"apc_paid":null,"fwci":3.0316,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.92715408,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"62","issue":"23","first_page":"5961","last_page":"5974"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9991999864578247,"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":0.9991000294685364,"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/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.75202476978302},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6665596961975098},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6372764110565186},{"id":"https://openalex.org/keywords/attention-network","display_name":"Attention network","score":0.6054612398147583},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4873669743537903},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46385762095451355},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4202178120613098},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3453145921230316},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33661913871765137},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3277326226234436},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1865445375442505}],"concepts":[{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.75202476978302},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6665596961975098},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6372764110565186},{"id":"https://openalex.org/C2993807640","wikidata":"https://www.wikidata.org/wiki/Q103709453","display_name":"Attention network","level":2,"score":0.6054612398147583},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4873669743537903},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46385762095451355},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4202178120613098},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3453145921230316},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33661913871765137},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3277326226234436},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1865445375442505},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.0}],"mesh":[{"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c01092","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01092","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36398714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36398714","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2021246780","display_name":null,"funder_award_id":"21CX06018A","funder_id":"https://openalex.org/F4320329878","funder_display_name":"Central University Basic Research Fund of China"},{"id":"https://openalex.org/G2494574696","display_name":"\u57fa\u4e8e\u8109\u51b2\u795e\u7ecf\u819c\u7cfb\u7edf\u7684\u6545\u969c\u8bca\u65ad\u6a21\u578b\u7814\u7a76","funder_award_id":"61672033","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2900616867","display_name":null,"funder_award_id":"2021YFA1000103","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"},{"id":"https://openalex.org/G4037723416","display_name":null,"funder_award_id":"61873280","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4302230499","display_name":null,"funder_award_id":"tsqn201812029","funder_id":"https://openalex.org/F4320326189","funder_display_name":"Taishan Scholar Project of Shandong Province"},{"id":"https://openalex.org/G6059194225","display_name":"\u57fa\u4e8e\u81ea\u5b66\u4e60\u8109\u51b2\u795e\u7ecf\u819c\u7cfb\u7edf\u7684\u65e9\u671f\u80ba\u764c\u5206\u578b\u667a\u80fd\u8bca\u65ad\u53ca\u5176\u5728\u4e34\u5e8a\u4e2d\u7684\u5e94\u7528\u7814\u7a76","funder_award_id":"61972416","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6638739136","display_name":"\u57fa\u4e8eDNA\u6298\u7eb8\u672f\u7684\u7eb3\u7c73\u5668\u4ef6\u7814\u7a76","funder_award_id":"61672248","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6683504761","display_name":null,"funder_award_id":"ZR2021QF023","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G6781294939","display_name":null,"funder_award_id":"2021YFA1000102","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"},{"id":"https://openalex.org/G8870393515","display_name":null,"funder_award_id":"ZR2019MF012","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null},{"id":"https://openalex.org/F4320326189","display_name":"Taishan Scholar Project of Shandong Province","ror":null},{"id":"https://openalex.org/F4320329878","display_name":"Central University Basic Research Fund of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1966716734","https://openalex.org/W2008708467","https://openalex.org/W2028258513","https://openalex.org/W2044055478","https://openalex.org/W2051210555","https://openalex.org/W2126103104","https://openalex.org/W2129834345","https://openalex.org/W2141234232","https://openalex.org/W2141627824","https://openalex.org/W2155194485","https://openalex.org/W2158714788","https://openalex.org/W2163879391","https://openalex.org/W2907063321","https://openalex.org/W2944679105","https://openalex.org/W2955690154","https://openalex.org/W2971405760","https://openalex.org/W2992752586","https://openalex.org/W3009202743","https://openalex.org/W3013976849","https://openalex.org/W3080498684","https://openalex.org/W3129073614","https://openalex.org/W3147254695","https://openalex.org/W3177500196","https://openalex.org/W3197696221","https://openalex.org/W4205989901","https://openalex.org/W4297179162"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4224009465","https://openalex.org/W4306674287","https://openalex.org/W4392094631","https://openalex.org/W4389995241","https://openalex.org/W4309362167","https://openalex.org/W4320149722","https://openalex.org/W3213655484","https://openalex.org/W2790921906","https://openalex.org/W2163612744"],"abstract_inverted_index":{"The":[0,83,96,114],"prediction":[1,153],"of":[2,20,32,159,236],"a":[3,10,57,81,129,213],"protein\u2013protein":[4],"interaction":[5],"site":[6,238],"(PPI":[7],"site)":[8],"plays":[9],"very":[11],"important":[12],"role":[13],"in":[14,26,92],"the":[15,27,30,33,76,90,93,119,123,141,145,152,157,166,180,185,198,206,220,224,233],"biochemical":[16],"process,":[17],"and":[18,39,66,107,134,172,203,230],"lots":[19],"computational":[21,48,59],"methods":[22,35,171],"have":[23],"been":[24],"proposed":[25],"past.":[28],"However,":[29],"majority":[31],"past":[34],"are":[36,109,116],"time":[37],"consuming":[38],"lack":[40],"accuracy.":[41],"Hence,":[42],"coming":[43],"up":[44],"with":[45,165],"an":[46],"effective":[47,229],"method":[49],"is":[50,78,149,228],"necessary.":[51],"In":[52,73],"this":[53],"article,":[54],"we":[55,127],"present":[56],"novel":[58],"model":[60,161,178],"called":[61],"RGN":[62],"(residue-based":[63],"graph":[64,94,131,135],"attention":[65,136],"convolutional":[67,132],"network)":[68],"to":[69,138,216],"predict":[70],"PPI":[71,237],"sites.":[72],"our":[74,160],"paper,":[75],"protein":[77,169,174,221,225],"treated":[79],"as":[80,89,111],"graph.":[82],"amino":[84,124],"acid":[85],"can":[86],"be":[87],"seen":[88],"node":[91,112,147],"structure.":[95],"position-specific":[97],"scoring":[98],"matrix,":[99],"hidden":[100],"Markov":[101],"model,":[102],"hydrogen":[103],"bond":[104],"estimation":[105],"algorithm,":[106],"ProtBert":[108],"applied":[110],"features.":[113],"edges":[115],"decided":[117],"by":[118,162],"spatial":[120],"distance":[121],"between":[122],"acids.":[125],"Then,":[126],"utilize":[128],"residue-based":[130],"network":[133,137],"further":[139],"extract":[140],"deeper":[142],"feature.":[143],"Finally,":[144],"processed":[146],"feature":[148],"fed":[150],"into":[151],"layer.":[154],"We":[155,210],"show":[156],"superiority":[158],"comparing":[163],"it":[164],"other":[167],"four":[168],"structure-based":[170],"five":[173],"sequence-based":[175],"methods.":[176],"Our":[177],"obtains":[179],"best":[181],"performance":[182],"on":[183],"all":[184],"evaluation":[186],"metrics":[187],"(accuracy,":[188],"precision,":[189],"recall,":[190],"F1":[191],"score,":[192],"Matthews":[193],"correlation":[194],"coefficient,":[195],"area":[196,204],"under":[197,205],"receiver":[199],"operating":[200],"characteristic":[201],"curve,":[202],"precision":[207],"recall":[208],"curve).":[209],"also":[211],"conduct":[212],"case":[214],"study":[215],"demonstrate":[217],"that":[218],"extracting":[219],"information":[222],"from":[223],"structure":[226],"perspective":[227],"points":[231],"out":[232],"difficult":[234],"aspect":[235],"prediction.":[239]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":5}],"updated_date":"2026-06-07T08:38:57.713557","created_date":"2025-10-10T00:00:00"}