{"id":"https://openalex.org/W7130652521","doi":"https://doi.org/10.1021/acs.jcim.5c02963","title":"RCLG-PPIS: Structure-Aware Protein\u2013Protein Interaction Site Prediction with Cascaded Local and Global Information","display_name":"RCLG-PPIS: Structure-Aware Protein\u2013Protein Interaction Site Prediction with Cascaded Local and Global Information","publication_year":2026,"publication_date":"2026-02-19","ids":{"openalex":"https://openalex.org/W7130652521","doi":"https://doi.org/10.1021/acs.jcim.5c02963","pmid":"https://pubmed.ncbi.nlm.nih.gov/41714906"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02963","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02963","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/A5100709936","display_name":"Jianzhong Chen","orcid":"https://orcid.org/0000-0002-8232-7298"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]},{"id":"https://openalex.org/I4210097554","display_name":"Center for Excellence in Brain Science and Intelligence Technology","ror":"https://ror.org/00vpwhm04","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210097554"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jing Chen","raw_affiliation_strings":["Jiangnan University","Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computing Intelligence","School of Artificial Intelligence and Computer Science"],"affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computing Intelligence","institution_ids":["https://openalex.org/I4210097554"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113364066","display_name":"Xiaobo Ge","orcid":"https://orcid.org/0000-0002-7802-0437"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaobo Ge","raw_affiliation_strings":["Jiangnan University","School of Artificial Intelligence and Computer Science"],"affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126508416","display_name":"Qiuyao Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiuyao Qi","raw_affiliation_strings":["Jiangnan University","School of Artificial Intelligence and Computer Science"],"affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100373113","display_name":"Heng Zhang","orcid":"https://orcid.org/0000-0002-0103-2173"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hengrui Zhang","raw_affiliation_strings":["Jiangnan University","School of Artificial Intelligence and Computer Science"],"affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5126486910","display_name":"Tingbin Luo","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingbin Luo","raw_affiliation_strings":["Jiangnan University","School of Artificial Intelligence and Computer Science"],"affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100709936"],"corresponding_institution_ids":["https://openalex.org/I111599522","https://openalex.org/I4210097554"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.66087939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"5","first_page":"2929","last_page":"2940"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6110000014305115,"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":0.6110000014305115,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.1039000004529953,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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":0.08129999786615372,"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/graph","display_name":"Graph","score":0.48829999566078186},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.46299999952316284},{"id":"https://openalex.org/keywords/residual","display_name":"Residual","score":0.41830000281333923},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4034999907016754},{"id":"https://openalex.org/keywords/laplacian-matrix","display_name":"Laplacian matrix","score":0.3977999985218048},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3952000141143799},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.3917999863624573},{"id":"https://openalex.org/keywords/cascade","display_name":"Cascade","score":0.36239999532699585}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7376000285148621},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5037999749183655},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.48829999566078186},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.46299999952316284},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4205000102519989},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.41830000281333923},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4034999907016754},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39809998869895935},{"id":"https://openalex.org/C115178988","wikidata":"https://www.wikidata.org/wiki/Q772067","display_name":"Laplacian matrix","level":3,"score":0.3977999985218048},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3952000141143799},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3917999863624573},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.36239999532699585},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.33640000224113464},{"id":"https://openalex.org/C2993807640","wikidata":"https://www.wikidata.org/wiki/Q103709453","display_name":"Attention network","level":2,"score":0.33559998869895935},{"id":"https://openalex.org/C2986090443","wikidata":"https://www.wikidata.org/wiki/Q77870413","display_name":"Local structure","level":2,"score":0.3222000002861023},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.3156999945640564},{"id":"https://openalex.org/C165700671","wikidata":"https://www.wikidata.org/wiki/Q203484","display_name":"Laplace operator","level":2,"score":0.29030001163482666},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.27410000562667847},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.26809999346733093},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26809999346733093},{"id":"https://openalex.org/C123138037","wikidata":"https://www.wikidata.org/wiki/Q5570871","display_name":"Global network","level":2,"score":0.25360000133514404},{"id":"https://openalex.org/C2982962833","wikidata":"https://www.wikidata.org/wiki/Q17092450","display_name":"Information fusion","level":2,"score":0.2500999867916107}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02963","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02963","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:41714906","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41714906","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":[{"id":"https://metadata.un.org/sdg/17","score":0.5136681795120239,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W2006433949","https://openalex.org/W2008708467","https://openalex.org/W2009672036","https://openalex.org/W2043699100","https://openalex.org/W2051210555","https://openalex.org/W2055043387","https://openalex.org/W2090703756","https://openalex.org/W2151148091","https://openalex.org/W2155194485","https://openalex.org/W2158714788","https://openalex.org/W2750875483","https://openalex.org/W2754800853","https://openalex.org/W2769328179","https://openalex.org/W2944679105","https://openalex.org/W2964015378","https://openalex.org/W2971405760","https://openalex.org/W2990458240","https://openalex.org/W3009202743","https://openalex.org/W3013976849","https://openalex.org/W3042770487","https://openalex.org/W3080498684","https://openalex.org/W3113177135","https://openalex.org/W3177500196","https://openalex.org/W3197696221","https://openalex.org/W4220952154","https://openalex.org/W4221149947","https://openalex.org/W4327550249","https://openalex.org/W4362522229","https://openalex.org/W4377968189","https://openalex.org/W4387242121","https://openalex.org/W4388407261","https://openalex.org/W4388663283","https://openalex.org/W4389076414","https://openalex.org/W4400520514","https://openalex.org/W4403580373","https://openalex.org/W4404207188","https://openalex.org/W4404210051","https://openalex.org/W4406238289","https://openalex.org/W4408129837","https://openalex.org/W4411393629"],"related_works":[],"abstract_inverted_index":{"Accurately":[0],"obtaining":[1],"Protein-protein":[2],"Interaction":[3],"Sites":[4],"(PPIS)":[5],"information":[6,48,70,93],"is":[7],"crucial":[8],"for":[9,64,74],"understanding":[10],"cell":[11],"functions":[12],"and":[13,45,91,109,196],"drug":[14],"development.":[15],"In":[16,76,112],"recent":[17],"years,":[18],"approaches":[19,41],"based":[20],"on":[21,28,174],"Graph":[22],"Neural":[23],"Networks":[24],"with":[25,88],"a":[26,52,81,136],"focus":[27],"local-global":[29,100],"collaborative":[30],"modeling":[31],"have":[32,72],"achieved":[33],"significant":[34],"advances":[35],"in":[36,57,194,198],"PPIS":[37],"prediction.":[38],"However,":[39],"existing":[40],"typically":[42],"process":[43],"local":[44,58,90,108,123],"global":[46,92,110,137],"structural":[47,125,158],"separately,":[49],"leading":[50],"to":[51,103,165],"lack":[53],"of":[54,69,127,170,192],"contextual":[55],"awareness":[56],"information.":[59,111],"Furthermore,":[60],"current":[61],"fusion":[62,106],"strategies":[63],"integrating":[65],"these":[66,141],"two":[67,142],"types":[68],"still":[71],"room":[73],"improvement.":[75],"this":[77],"study,":[78],"we":[79,153],"propose":[80],"novel":[82],"structure-aware":[83],"protein-protein":[84],"interaction":[85],"site":[86],"prediction":[87],"cascaded":[89],"(RCLG-PPIS).":[94],"Specifically,":[95],"RCLG-PPIS":[96,182],"employs":[97],"residual":[98],"cascade":[99],"(RCLG)":[101],"module":[102],"strengthen":[104],"the":[105,146,155,162,167,175],"between":[107],"RCLG":[113],"module,":[114],"an":[115],"E(n)":[116],"equivariant":[117],"graph":[118],"neural":[119],"network":[120],"(EGNN)":[121],"extracts":[122],"3D":[124],"features":[126,164],"proteins,":[128],"while":[129],"transformer":[130,144],"captures":[131],"long-range":[132],"residue":[133],"dependencies":[134],"from":[135],"perspective.":[138],"By":[139],"cascading":[140],"components,":[143],"helps":[145],"EGNN":[147],"expand":[148],"its":[149],"receptive":[150],"field.":[151],"Additionally,":[152],"integrate":[154],"Laplacian":[156],"eigenvectors":[157],"encoder":[159],"(LapSE)":[160],"into":[161],"node":[163],"enhance":[166],"predictive":[168],"capability":[169],"RCLG-PPIS.":[171],"Experimental":[172],"results":[173],"benchmark":[176],"data":[177],"set":[178],"(Test_60)":[179],"demonstrate":[180],"that":[181],"outperforms":[183],"state-of-the-art":[184],"models":[185],"across":[186],"multiple":[187],"metrics,":[188],"achieving":[189],"notable":[190],"improvements":[191],"6.38%":[193],"AUPRC,":[195],"8.80%":[197],"MCC.":[199]},"counts_by_year":[],"updated_date":"2026-03-12T06:13:28.667946","created_date":"2026-02-20T00:00:00"}
