{"id":"https://openalex.org/W4415298146","doi":"https://doi.org/10.1093/bib/bbaf544","title":"Enhancing cross-domain protein and peptide interaction with retrained deep learning models","display_name":"Enhancing cross-domain protein and peptide interaction with retrained deep learning models","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4415298146","doi":"https://doi.org/10.1093/bib/bbaf544","pmid":"https://pubmed.ncbi.nlm.nih.gov/41104808"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf544","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf544","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Xin Cao","orcid":"https://orcid.org/0009-0001-6200-7203"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Cao","raw_affiliation_strings":["School of Data Science , The Chinese University of Hong Kong, Shenzhen 518172,"],"raw_orcid":"https://orcid.org/0009-0001-6200-7203","affiliations":[{"raw_affiliation_string":"School of Data Science , The Chinese University of Hong Kong, Shenzhen 518172,","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110931721","display_name":"Jingquan Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingquan Li","raw_affiliation_strings":["School of Data Science , The Chinese University of Hong Kong, Shenzhen 518172,"],"raw_orcid":"https://orcid.org/0009-0000-5516-9709","affiliations":[{"raw_affiliation_string":"School of Data Science , The Chinese University of Hong Kong, Shenzhen 518172,","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fanpeng Meng","orcid":"https://orcid.org/0009-0000-1037-2164"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fanpeng Meng","raw_affiliation_strings":["School of Science and Engineering , The Chinese University of Hong Kong, Shenzhen 518172,"],"raw_orcid":"https://orcid.org/0009-0000-1037-2164","affiliations":[{"raw_affiliation_string":"School of Science and Engineering , The Chinese University of Hong Kong, Shenzhen 518172,","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Bing Yang","orcid":"https://orcid.org/0000-0002-1183-3708"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bing Yang","raw_affiliation_strings":["College of Veterinary Medicine , Huazhong Agricultural University, Wuhan 430070,","State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University, Wuhan 430070,"],"raw_orcid":"https://orcid.org/0000-0002-1183-3708","affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine , Huazhong Agricultural University, Wuhan 430070,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University, Wuhan 430070,","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015878350","display_name":"Yanyan Zou","orcid":"https://orcid.org/0000-0002-7051-4547"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210145292","display_name":"Shenzhen University Health Science Center","ror":"https://ror.org/04yjbr930","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145292"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yanyan Zou","raw_affiliation_strings":["Center for Cell Lineage Technology and Engineering , Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530,","College of Information , Huazhong Agricultural University, Wuhan 430070,","Faculty of Life and Health Sciences , Shenzhen University of Advanced Technology, Shenzhen 518060,","State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University, Wuhan 430070,"],"raw_orcid":"https://orcid.org/0000-0002-7051-4547","affiliations":[{"raw_affiliation_string":"Center for Cell Lineage Technology and Engineering , Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"College of Information , Huazhong Agricultural University, Wuhan 430070,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Faculty of Life and Health Sciences , Shenzhen University of Advanced Technology, Shenzhen 518060,","institution_ids":["https://openalex.org/I4210145292","https://openalex.org/I4210152380"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology , Huazhong Agricultural University, Wuhan 430070,","institution_ids":["https://openalex.org/I204823248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5015878350"],"corresponding_institution_ids":["https://openalex.org/I204823248","https://openalex.org/I2802148028","https://openalex.org/I4210145292","https://openalex.org/I4210152380"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.4913,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.86231105,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973000288009644,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.996999979019165,"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/overfitting","display_name":"Overfitting","score":0.9097999930381775},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.7498999834060669},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5285000205039978},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5260999798774719},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.47029998898506165},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4316999912261963},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4052000045776367},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.36660000681877136},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.35670000314712524}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.9097999930381775},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.757099986076355},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7498999834060669},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6722000241279602},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5285000205039978},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5260999798774719},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5072000026702881},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.47029998898506165},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4316999912261963},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42170000076293945},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4052000045776367},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.36660000681877136},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.35670000314712524},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3400999903678894},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3393000066280365},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.33180001378059387},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.33059999346733093},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.32899999618530273},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.3102000057697296},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.29899999499320984},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.2870999872684479},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.27619999647140503},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.2538999915122986},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.25380000472068787},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2531000077724457},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.25279998779296875}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"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":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf544","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41104808","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41104808","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11339982","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12531998","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf544","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf544","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6876888337","display_name":null,"funder_award_id":"32330104","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":64,"referenced_works":["https://openalex.org/W1803102843","https://openalex.org/W1975118394","https://openalex.org/W1980725116","https://openalex.org/W1992006348","https://openalex.org/W2009313526","https://openalex.org/W2030204844","https://openalex.org/W2032902055","https://openalex.org/W2037036397","https://openalex.org/W2054989124","https://openalex.org/W2056335234","https://openalex.org/W2076710572","https://openalex.org/W2084619201","https://openalex.org/W2099862356","https://openalex.org/W2120973253","https://openalex.org/W2136957665","https://openalex.org/W2147097971","https://openalex.org/W2152705149","https://openalex.org/W2156125289","https://openalex.org/W2167869241","https://openalex.org/W2170747616","https://openalex.org/W2170861153","https://openalex.org/W2176618995","https://openalex.org/W2213532196","https://openalex.org/W2255955546","https://openalex.org/W2264399954","https://openalex.org/W2329901740","https://openalex.org/W2337686908","https://openalex.org/W2344144945","https://openalex.org/W2513180055","https://openalex.org/W2570408261","https://openalex.org/W2739980134","https://openalex.org/W2744103888","https://openalex.org/W2809147071","https://openalex.org/W2885583144","https://openalex.org/W2957436444","https://openalex.org/W2971405760","https://openalex.org/W2995514860","https://openalex.org/W3000577518","https://openalex.org/W3042398970","https://openalex.org/W3043299403","https://openalex.org/W3087769169","https://openalex.org/W3120019274","https://openalex.org/W3134169372","https://openalex.org/W3136918052","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3199468887","https://openalex.org/W3199607358","https://openalex.org/W3202105508","https://openalex.org/W3209465832","https://openalex.org/W4205177317","https://openalex.org/W4226343290","https://openalex.org/W4280617006","https://openalex.org/W4296293027","https://openalex.org/W4301372783","https://openalex.org/W4307645443","https://openalex.org/W4308834893","https://openalex.org/W4311788484","https://openalex.org/W4323807094","https://openalex.org/W4362663312","https://openalex.org/W4367049415","https://openalex.org/W4385405823","https://openalex.org/W4387077017","https://openalex.org/W4409229134"],"related_works":[],"abstract_inverted_index":{"Accumulating":[0],"evidence":[1],"has":[2],"shown":[3],"that":[4],"protein-peptide":[5],"interactions":[6],"(PPepIs)":[7],"are":[8],"critical":[9],"for":[10,168],"understanding":[11],"biological":[12],"processes":[13],"and":[14,32,77,80,94,112,128,159,163],"developing":[15],"peptide-based":[16],"therapeutics.":[17],"While":[18],"deep":[19,84],"learning-based":[20],"protein-protein":[21],"interaction":[22],"(PPI)":[23],"prediction":[24],"showed":[25],"promise,":[26],"it":[27],"suffers":[28],"from":[29,62],"poor":[30],"generalization":[31],"overfitting":[33],"problems.":[34],"This":[35],"study":[36],"addresses":[37],"these":[38],"challenges":[39],"by":[40],"focusing":[41],"training":[42,71,99],"on":[43,88,100],"short":[44],"proteins":[45,127],"containing":[46],"much":[47],"less":[48],"redundant":[49],"noninteracting":[50],"sequence.":[51],"To":[52],"avoid":[53],"artificial":[54],"PPI,":[55],"only":[56],"the":[57,69,106],"experimentally":[58],"validated":[59],"PPI":[60,70,115],"pairs":[61],"STRING":[63],"database":[64],"were":[65],"used":[66],"to":[67,108,149,154],"construct":[68],"dataset.":[72],"We":[73],"integrated":[74],"protein":[75,111],"sequence":[76],"structure":[78],"information":[79],"presented":[81],"a":[82],"multilevel":[83],"learning":[85],"framework.":[86],"Training":[87],"short-protein":[89],"datasets":[90],"yielded":[91],"higher":[92],"accuracy":[93],"computational":[95],"efficiency":[96],"compared":[97],"with":[98,125],"long-protein":[101],"datasets.":[102],"Moreover,":[103],"we":[104,118],"applied":[105,148],"model":[107,144],"delineate":[109,150],"human":[110,126],"SARS-CoV-2":[113,129],"virus":[114],"networks.":[116],"Notably,":[117],"screened":[119],"PPepIs":[120],"of":[121],"current":[122],"drug":[123,156],"peptides":[124],"viral":[130,169],"proteins,":[131],"identifying":[132],"numerous":[133],"potential":[134],"side":[135,160],"effect":[136,161],"or":[137],"new":[138],"therapeutic":[139],"targets.":[140],"Together,":[141],"our":[142],"retrained":[143],"could":[145],"be":[146],"extensively":[147],"PPepI":[151],"network,":[152],"contribute":[153],"peptide":[155],"target":[157],"identification":[158],"analysis,":[162],"also":[164],"provide":[165],"ample":[166],"resource":[167],"infection":[170],"investigations.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-18T00:00:00"}
