{"id":"https://openalex.org/W7137884146","doi":"https://doi.org/10.1021/acs.jcim.5c03139","title":"HGT-PepPI: A Heterogeneous Graph-Based Framework Leveraging Pragmatic Analysis for Peptide\u2013Protein Interaction Prediction","display_name":"HGT-PepPI: A Heterogeneous Graph-Based Framework Leveraging Pragmatic Analysis for Peptide\u2013Protein Interaction Prediction","publication_year":2026,"publication_date":"2026-03-17","ids":{"openalex":"https://openalex.org/W7137884146","doi":"https://doi.org/10.1021/acs.jcim.5c03139","pmid":"https://pubmed.ncbi.nlm.nih.gov/41841204"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c03139","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c03139","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/A5129732442","display_name":"Ke Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ke Yan","raw_affiliation_strings":["Beijing Institute of Technology","School of Computer Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tianyi Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianyi Liu","raw_affiliation_strings":["Beijing Institute of Technology","School of Computer Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129658749","display_name":"Xinxin Zhan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119028","display_name":"Beijing Anzhen Hospital","ror":"https://ror.org/02h2j1586","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210119028"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xinxin Zhan","raw_affiliation_strings":["Capital Medical University, Beijing Anzhen Hospital","Department of Dentistry"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Capital Medical University, Beijing Anzhen Hospital","institution_ids":["https://openalex.org/I4210119028"]},{"raw_affiliation_string":"Department of Dentistry","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121477698","display_name":"Shutao Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shutao Chen","raw_affiliation_strings":["Beijing Institute of Technology","School of Computer Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111078324","display_name":"Moran Li","orcid":"https://orcid.org/0000-0002-6406-1983"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meijing Li","raw_affiliation_strings":["Beijing Institute of Technology","School of Computer Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129685381","display_name":"Tianqi Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianqi Hu","raw_affiliation_strings":["Beijing Institute of Technology","School of Computer Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129683874","display_name":"Bin Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4210099974","display_name":"Intelligent Light (United States)","ror":"https://ror.org/00wqezk94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099974"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Bin Liu","raw_affiliation_strings":["Beijing Institute of Technology","Beijing Key Laboratory of Lightweight Intelligent System","School of Computer Science and Technology"],"raw_orcid":"https://orcid.org/0000-0002-8520-8374","affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"Beijing Key Laboratory of Lightweight Intelligent System","institution_ids":["https://openalex.org/I4210099974"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5129658749","https://openalex.org/A5129683874"],"corresponding_institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4210099974","https://openalex.org/I4210119028","https://openalex.org/I4390039265"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.58154912,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"7","first_page":"4232","last_page":"4244"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5347999930381775,"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":0.5347999930381775,"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":0.15299999713897705,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.10980000346899033,"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/generalization","display_name":"Generalization","score":0.7095000147819519},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5464000105857849},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5311999917030334},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5094000101089478},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4146000146865845},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.39890000224113464},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.3864000141620636},{"id":"https://openalex.org/keywords/alanine-scanning","display_name":"Alanine scanning","score":0.3635999858379364}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7825999855995178},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.7095000147819519},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5464000105857849},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5311999917030334},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5094000101089478},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5026999711990356},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48159998655319214},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4146000146865845},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40459999442100525},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.39890000224113464},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.3864000141620636},{"id":"https://openalex.org/C2780227090","wikidata":"https://www.wikidata.org/wiki/Q2636892","display_name":"Alanine scanning","level":5,"score":0.3635999858379364},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34940001368522644},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.3382999897003174},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3179999887943268},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3093000054359436},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3070000112056732},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.30169999599456787},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2996000051498413},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.29280000925064087},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.27889999747276306},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.2621000111103058},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2531999945640564},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.25279998779296875}],"mesh":[{"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":"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c03139","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c03139","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:41841204","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41841204","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":[{"score":0.56065434217453,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G5263694324","display_name":null,"funder_award_id":"62325202","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5600204614","display_name":null,"funder_award_id":"L248013","funder_id":"https://openalex.org/F4320334977","funder_display_name":"Beijing Municipal Natural Science Foundation"},{"id":"https://openalex.org/G6351260564","display_name":null,"funder_award_id":"62271049","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6728619461","display_name":null,"funder_award_id":"62473049","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7894669521","display_name":null,"funder_award_id":"U22A2039","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/F4320327514","display_name":"Beijing Institute of Technology Research Fund Program for Young Scholars","ror":null},{"id":"https://openalex.org/F4320334977","display_name":"Beijing Municipal Natural Science Foundation","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1979798177","https://openalex.org/W1993046136","https://openalex.org/W2025816743","https://openalex.org/W2093205346","https://openalex.org/W2096495474","https://openalex.org/W2125910575","https://openalex.org/W2158714788","https://openalex.org/W2592644437","https://openalex.org/W2806884808","https://openalex.org/W2839764993","https://openalex.org/W2902812092","https://openalex.org/W2947612926","https://openalex.org/W2948988173","https://openalex.org/W2949301320","https://openalex.org/W3019745511","https://openalex.org/W3115467422","https://openalex.org/W3125047599","https://openalex.org/W3136827720","https://openalex.org/W3159177617","https://openalex.org/W3177500196","https://openalex.org/W3194835771","https://openalex.org/W3199607358","https://openalex.org/W3216624979","https://openalex.org/W4255501777","https://openalex.org/W4281557145","https://openalex.org/W4309218736","https://openalex.org/W4317931114","https://openalex.org/W4318981550","https://openalex.org/W4320495200","https://openalex.org/W4321003857","https://openalex.org/W4321015480","https://openalex.org/W4321851522","https://openalex.org/W4323352404","https://openalex.org/W4360999048","https://openalex.org/W4366089579","https://openalex.org/W4381432349","https://openalex.org/W4387033830","https://openalex.org/W4387780855","https://openalex.org/W4388080288","https://openalex.org/W4389526560","https://openalex.org/W4390946589","https://openalex.org/W4396912374","https://openalex.org/W4400061043","https://openalex.org/W4400576356","https://openalex.org/W4401009488","https://openalex.org/W4401435582","https://openalex.org/W4402053335","https://openalex.org/W4402947492","https://openalex.org/W4403122920","https://openalex.org/W4403782367","https://openalex.org/W4403782504","https://openalex.org/W4403907284","https://openalex.org/W4404505690","https://openalex.org/W4404650713","https://openalex.org/W4405525278","https://openalex.org/W4406677312","https://openalex.org/W4408129839","https://openalex.org/W4408717486","https://openalex.org/W4410285152","https://openalex.org/W4410991318","https://openalex.org/W4411891367","https://openalex.org/W4412650705","https://openalex.org/W4412929243"],"related_works":[],"abstract_inverted_index":{"Peptide-Protein":[0],"Interactions":[1],"(PepPIs)":[2],"are":[3,94,110],"essential":[4],"to":[5,33,63,72,161,216],"a":[6,81,131,174,206],"wide":[7],"range":[8],"of":[9,41,68,138,150,177,230],"biological":[10,139],"processes,":[11],"including":[12],"gene":[13],"regulation,":[14],"cellular":[15],"homeostasis,":[16],"and":[17,70,91,120,126,167,194,205,220,227],"metabolic":[18],"modulation.":[19],"Researchers":[20],"have":[21],"developed":[22],"several":[23],"computational":[24,43],"deep":[25],"learning":[26,147],"predictors":[27],"based":[28],"on":[29],"the":[30,35,38,48,53,65,103,154,158,163,186,213],"sequence":[31,114,165],"information":[32],"predict":[34,73],"PepPIs.":[36,74],"However,":[37],"generalization":[39,145],"performance":[40,193],"most":[42],"methods":[44],"is":[45,61],"constrained":[46],"by":[47,112,146],"limited":[49],"protein-peptide":[50],"complexes":[51],"in":[52,190],"RCSB":[54],"Protein":[55],"Data":[56],"Bank":[57],"database.":[58],"Moreover,":[59,153],"it":[60],"challenging":[62],"utilize":[64],"complex":[66,169],"context":[67],"proteins":[69,125],"peptides":[71],"In":[75,196],"this":[76],"study,":[77],"we":[78,198],"propose":[79],"HGT-PepPI,":[80],"heterogeneous":[82,97],"graph-based":[83],"framework":[84],"designed":[85,199],"for":[86],"PepPIs":[87],"prediction.":[88],"The":[89,106,225],"peptide":[90,222],"protein":[92],"sequences":[93],"initialized":[95],"as":[96],"nodes":[98],"with":[99],"semantic":[100,115],"representations":[101],"using":[102],"ProtT5":[104],"model.":[105],"three":[107],"multirelational":[108],"edges":[109],"constructed":[111],"integrating":[113],"information,":[116,140],"evolutionary":[117],"conservation":[118],"profiles,":[119],"experimentally":[121],"validated":[122],"interactions":[123],"between":[124],"peptides,":[127],"respectively.":[128],"By":[129],"constructing":[130],"graph":[132],"that":[133,183],"inherently":[134],"integrates":[135],"multiple":[136],"types":[137],"our":[141],"method":[142,156],"achieves":[143],"superior":[144],"transferable":[148],"patterns":[149],"interaction":[151,178],"semantics.":[152,179],"proposed":[155],"employs":[157],"message-passing":[159],"operations":[160],"capture":[162],"local":[164],"characteristics":[166],"global":[168],"contextual":[170],"dependencies,":[171],"thereby":[172],"enabling":[173],"comprehensive":[175],"modeling":[176],"Experimental":[180],"results":[181],"demonstrate":[182],"HGT-PepPI":[184,231],"outperforms":[185],"existing":[187],"state-of-the-art":[188],"approaches":[189],"both":[191],"predictive":[192],"robustness.":[195],"addition,":[197],"an":[200],"alanine":[201],"scanning":[202],"mutagenesis":[203],"experiment":[204],"binding":[207],"affinity":[208],"experiment,":[209],"which":[210],"successfully":[211],"verified":[212],"model's":[214],"ability":[215],"identify":[217],"key":[218],"residues":[219],"guide":[221],"drug":[223],"design.":[224],"data":[226],"source":[228],"code":[229],"can":[232],"be":[233],"publicly":[234],"accessible":[235],"via":[236],"http://bliulab.net/HGT-PepPI.":[237]},"counts_by_year":[],"updated_date":"2026-04-14T06:02:45.956762","created_date":"2026-03-18T00:00:00"}