{"id":"https://openalex.org/W4414345646","doi":"https://doi.org/10.1021/acs.jcim.5c01390","title":"PPAP: A Protein\u2013protein Affinity Predictor Incorporating Interfacial Contact-Aware Attention","display_name":"PPAP: A Protein\u2013protein Affinity Predictor Incorporating Interfacial Contact-Aware Attention","publication_year":2025,"publication_date":"2025-09-19","ids":{"openalex":"https://openalex.org/W4414345646","doi":"https://doi.org/10.1021/acs.jcim.5c01390","pmid":"https://pubmed.ncbi.nlm.nih.gov/40970903"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01390","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01390","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/A5078558633","display_name":"Jie Qian","orcid":"https://orcid.org/0000-0002-6542-0677"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Qian","raw_affiliation_strings":["Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100429578","display_name":"Lin Yang","orcid":"https://orcid.org/0000-0003-1550-5792"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Yang","raw_affiliation_strings":["Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111729560","display_name":"Zhen Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210091809","display_name":"Shanghai Third People's Hospital","ror":"https://ror.org/00gp99k74","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210091809"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Duan","raw_affiliation_strings":["Shanghai TopScience Co., Ltd., No.238 the Third Jiang-Chang Road, Shanghai 200436, People\u2019s Republic of China","Shanghai TopScience Co., Ltd., No.238 the Third Jiang-Chang Road, Shanghai 200436, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai TopScience Co., Ltd., No.238 the Third Jiang-Chang Road, Shanghai 200436, People\u2019s Republic of China","institution_ids":["https://openalex.org/I4210091809"]},{"raw_affiliation_string":"Shanghai TopScience Co., Ltd., No.238 the Third Jiang-Chang Road, Shanghai 200436, People's Republic of China","institution_ids":["https://openalex.org/I4210091809"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016374232","display_name":"Renxiao Wang","orcid":"https://orcid.org/0000-0003-0485-0259"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Renxiao Wang","raw_affiliation_strings":["Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China"],"raw_orcid":"https://orcid.org/0000-0003-0485-0259","affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101708276","display_name":"Yifei Qi","orcid":"https://orcid.org/0000-0003-2853-7910"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yifei Qi","raw_affiliation_strings":["Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China"],"raw_orcid":"https://orcid.org/0000-0003-2853-7910","affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People\u2019s Republic of China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016374232","https://openalex.org/A5101708276"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":null,"apc_paid":null,"fwci":0.9736,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.7674464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"65","issue":"19","first_page":"9987","last_page":"9998"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9958999752998352,"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":0.9958999752998352,"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/T10617","display_name":"Cellular transport and secretion","score":0.9739000201225281,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T13127","display_name":"Biotin and Related Studies","score":0.9684000015258789,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/sequence","display_name":"Sequence (biology)","score":0.5594000220298767},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5450999736785889},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.46869999170303345},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.3977000117301941},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.3767000138759613},{"id":"https://openalex.org/keywords/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.36410000920295715},{"id":"https://openalex.org/keywords/correlation-coefficient","display_name":"Correlation coefficient","score":0.33239999413490295}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6736999750137329},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5594000220298767},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5450999736785889},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.536899983882904},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.46869999170303345},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44850000739097595},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.3977000117301941},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.3767000138759613},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3702000081539154},{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.36410000920295715},{"id":"https://openalex.org/C2780092901","wikidata":"https://www.wikidata.org/wiki/Q3433612","display_name":"Correlation coefficient","level":2,"score":0.33239999413490295},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.32919999957084656},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32910001277923584},{"id":"https://openalex.org/C55078378","wikidata":"https://www.wikidata.org/wiki/Q1136628","display_name":"Pearson product-moment correlation coefficient","level":2,"score":0.2985999882221222},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2806999981403351},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.2703000009059906},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.2597000002861023},{"id":"https://openalex.org/C3018069271","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Structural protein","level":3,"score":0.25450000166893005}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c01390","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01390","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:40970903","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40970903","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/G1108311842","display_name":null,"funder_award_id":"22033001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1413276435","display_name":null,"funder_award_id":"25JS2830200","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G1872111637","display_name":null,"funder_award_id":"22537001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5427963596","display_name":null,"funder_award_id":"82173739","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8121308808","display_name":null,"funder_award_id":"22373020","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/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1915490970","https://openalex.org/W1989527063","https://openalex.org/W1992006348","https://openalex.org/W2016894211","https://openalex.org/W2018337406","https://openalex.org/W2045870710","https://openalex.org/W2051710717","https://openalex.org/W2081598613","https://openalex.org/W2089914004","https://openalex.org/W2092285329","https://openalex.org/W2107936878","https://openalex.org/W2113442785","https://openalex.org/W2130479394","https://openalex.org/W2252854990","https://openalex.org/W2506377511","https://openalex.org/W2512372054","https://openalex.org/W2529398090","https://openalex.org/W2554019130","https://openalex.org/W2750861909","https://openalex.org/W2765949636","https://openalex.org/W2774509494","https://openalex.org/W2953103783","https://openalex.org/W2974982237","https://openalex.org/W2992752586","https://openalex.org/W2995387264","https://openalex.org/W3082498841","https://openalex.org/W3177828909","https://openalex.org/W3179485843","https://openalex.org/W3202105508","https://openalex.org/W3209839278","https://openalex.org/W3211728297","https://openalex.org/W3216094319","https://openalex.org/W4214632301","https://openalex.org/W4214886481","https://openalex.org/W4220765272","https://openalex.org/W4226155533","https://openalex.org/W4248633161","https://openalex.org/W4281742422","https://openalex.org/W4283646162","https://openalex.org/W4296293027","https://openalex.org/W4323543778","https://openalex.org/W4327550249","https://openalex.org/W4375856225","https://openalex.org/W4385707729","https://openalex.org/W4387303685","https://openalex.org/W4388092799","https://openalex.org/W4388667159","https://openalex.org/W4389614980","https://openalex.org/W4389988233","https://openalex.org/W4390740784","https://openalex.org/W4392360559","https://openalex.org/W4396721167","https://openalex.org/W4396771497","https://openalex.org/W4399037948","https://openalex.org/W4399262081","https://openalex.org/W4401945308","https://openalex.org/W4404142756","https://openalex.org/W4404505690","https://openalex.org/W4404970143","https://openalex.org/W4406440058"],"related_works":[],"abstract_inverted_index":{"Protein\u2013protein":[0],"interactions":[1],"(PPIs)":[2],"play":[3],"fundamental":[4],"roles":[5],"in":[6,29,159],"biological":[7],"processes":[8],"and":[9,23,56],"therapeutic":[10],"development.":[11],"Accurately":[12],"predicting":[13],"PPI":[14],"binding":[15],"affinity":[16,46],"is":[17],"critical":[18],"for":[19,44,181,186],"understanding":[20],"interaction":[21,64],"mechanisms":[22],"guiding":[24],"protein":[25,141,182,191],"engineering.":[26],"Recent":[27],"advances":[28],"structure":[30],"prediction":[31,95,151],"like":[32],"AlphaFold":[33],"have":[34],"enabled":[35],"accurate":[36],"modeling":[37],"of":[38,190],"protein\u2013protein":[39],"complexes,":[40],"creating":[41],"new":[42],"opportunities":[43],"structure-based":[45],"prediction.":[47,167],"However,":[48],"existing":[49],"methods":[50],"predominantly":[51],"rely":[52],"on":[53,108,165],"sequence":[54,83],"information":[55],"fail":[57],"to":[58,157,161],"fully":[59],"exploit":[60],"structural":[61,80],"insights":[62],"at":[63],"interfaces.":[65],"To":[66],"address":[67],"this":[68],"gap,":[69],"we":[70,144],"propose":[71],"PPAP,":[72],"a":[73,127,176,187],"novel":[74],"deep":[75],"learning":[76],"framework":[77],"that":[78,147],"integrates":[79],"features":[81],"with":[82],"representations":[84],"through":[85],"an":[86],"interfacial":[87],"contact-aware":[88],"attention":[89],"mechanism.":[90],"Our":[91],"model":[92,125],"demonstrated":[93],"superior":[94],"performance":[96],"across":[97],"all":[98,137],"evaluated":[99],"data":[100],"sets,":[101],"outperforming":[102],"strong":[103],"sequence-based":[104],"large":[105],"language":[106],"models":[107],"the":[109,120,162],"internal":[110],"test":[111,122],"(":[112,132],"R":[113,133],"=":[114,117,134],"0.540,":[115],"MAE":[116],"1.546).":[118],"On":[119],"external":[121],"set,":[123],"our":[124,149],"achieved":[126],"higher":[128],"Pearson":[129],"correlation":[130],"coefficient":[131],"0.63)":[135],"than":[136],"benchmarked":[138],"models.":[139],"In":[140],"binder":[142],"design,":[143],"further":[145],"demonstrate":[146],"incorporating":[148],"model\u2019s":[150],"can":[152],"enhance":[153],"enrichment":[154],"by":[155],"up":[156],"10-fold":[158],"comparison":[160],"metrics":[163],"based":[164],"AlphaFold-Multimer":[166],"Given":[168],"its":[169],"robust":[170],"performance,":[171],"PPAP":[172],"holds":[173],"promise":[174],"as":[175],"valuable":[177],"tool":[178],"not":[179],"only":[180],"design":[183],"but":[184],"also":[185],"wide":[188],"range":[189],"interaction-related":[192],"applications.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-06-14T06:11:07.267592","created_date":"2025-10-10T00:00:00"}
