{"id":"https://openalex.org/W4413561658","doi":"https://doi.org/10.1021/acs.jcim.5c01713","title":"PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide\u2013Protein Interaction Prediction","display_name":"PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide\u2013Protein Interaction Prediction","publication_year":2025,"publication_date":"2025-08-25","ids":{"openalex":"https://openalex.org/W4413561658","doi":"https://doi.org/10.1021/acs.jcim.5c01713","pmid":"https://pubmed.ncbi.nlm.nih.gov/40854162"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01713","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01713","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/A5048926132","display_name":"Shizhuo Li","orcid":"https://orcid.org/0009-0008-1485-9840"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Shuaiyan Li","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":"https://orcid.org/0009-0008-4420-3295","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068273646","display_name":"Xiaorui Wang","orcid":"https://orcid.org/0000-0001-6893-2013"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Xiaorui Wang","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":"https://orcid.org/0000-0001-6893-2013","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020581357","display_name":"Yuchen Zhu","orcid":"https://orcid.org/0000-0001-5148-8569"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Yuchen Zhu","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114163404","display_name":"Jingxuan Ge","orcid":"https://orcid.org/0009-0006-9835-5660"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Jingxuan Ge","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109396412","display_name":"Donghai Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Donghai Zhao","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100569815","display_name":"Hongxia Xu","orcid":"https://orcid.org/0009-0003-9933-3998"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":true,"raw_author_name":"Hongxia Xu","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028525523","display_name":"Tingjun Hou","orcid":"https://orcid.org/0000-0001-7227-2580"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":true,"raw_author_name":"Tingjun Hou","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":"https://orcid.org/0000-0001-7227-2580","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008663435","display_name":"Chang\u2010Yu Hsieh","orcid":"https://orcid.org/0000-0002-6242-4218"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","CZ"],"is_corresponding":true,"raw_author_name":"Chang-Yu Hsieh","raw_affiliation_strings":["College of Pharmaceutical Sciences","Zhejiang University"],"raw_orcid":"https://orcid.org/0000-0002-6242-4218","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences","institution_ids":["https://openalex.org/I4210160211"]},{"raw_affiliation_string":"Zhejiang University","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5008663435","https://openalex.org/A5028525523","https://openalex.org/A5100569815"],"corresponding_institution_ids":["https://openalex.org/I4210160211","https://openalex.org/I76130692"],"apc_list":null,"apc_paid":null,"fwci":1.7708,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.87615316,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"65","issue":"17","first_page":"9061","last_page":"9074"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9976000189781189,"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":0.9951000213623047,"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/computer-science","display_name":"Computer science","score":0.6632422208786011},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5371478199958801},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5342812538146973},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5223632454872131},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49078449606895447},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.46423712372779846},{"id":"https://openalex.org/keywords/adversarial-system","display_name":"Adversarial system","score":0.4447084367275238},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.41048625111579895},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.28005897998809814},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09729743003845215}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6632422208786011},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5371478199958801},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5342812538146973},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5223632454872131},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49078449606895447},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.46423712372779846},{"id":"https://openalex.org/C37736160","wikidata":"https://www.wikidata.org/wiki/Q1801315","display_name":"Adversarial system","level":2,"score":0.4447084367275238},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.41048625111579895},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.28005897998809814},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09729743003845215},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"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":"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c01713","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01713","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:40854162","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40854162","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W2046219181","https://openalex.org/W2066852475","https://openalex.org/W2089731808","https://openalex.org/W2156125289","https://openalex.org/W2264362083","https://openalex.org/W2609643846","https://openalex.org/W2612935389","https://openalex.org/W2620998958","https://openalex.org/W2860192827","https://openalex.org/W2898364362","https://openalex.org/W2947305153","https://openalex.org/W2957436444","https://openalex.org/W2978840913","https://openalex.org/W2997482957","https://openalex.org/W2999044305","https://openalex.org/W3004238495","https://openalex.org/W3006242222","https://openalex.org/W3082081167","https://openalex.org/W3087769169","https://openalex.org/W3093053585","https://openalex.org/W3153418506","https://openalex.org/W3198168376","https://openalex.org/W3199468887","https://openalex.org/W3199607358","https://openalex.org/W3212051308","https://openalex.org/W4200182440","https://openalex.org/W4281557145","https://openalex.org/W4286500588","https://openalex.org/W4308834893","https://openalex.org/W4310461505","https://openalex.org/W4310494058","https://openalex.org/W4318981550","https://openalex.org/W4382982095","https://openalex.org/W4388621595","https://openalex.org/W4388845139","https://openalex.org/W4388979610","https://openalex.org/W4389259925","https://openalex.org/W4392804617","https://openalex.org/W4395093930","https://openalex.org/W4396721167","https://openalex.org/W4396813784","https://openalex.org/W4399716545","https://openalex.org/W4401418198","https://openalex.org/W4404035653","https://openalex.org/W4405035146","https://openalex.org/W4408315457","https://openalex.org/W4408564503","https://openalex.org/W4410621619","https://openalex.org/W4413107336"],"related_works":["https://openalex.org/W2502115930","https://openalex.org/W2482350142","https://openalex.org/W4246396837","https://openalex.org/W3126451824","https://openalex.org/W1561927205","https://openalex.org/W3191453585","https://openalex.org/W4297672492","https://openalex.org/W4310988119","https://openalex.org/W4285226279","https://openalex.org/W4288019534"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1,208,238],"of":[2,28,36,100,113,126,133,151,193,251],"the":[3,26,33,37,65,88,111,124,131,138,148,164,191,247],"peptide-protein":[4,139,181],"interaction":[5],"(PepPI)":[6],"is":[7,115],"crucial":[8],"for":[9,40,54,80,258,270],"developing":[10],"peptide-based":[11,272],"therapeutics":[12],"and":[13,73,85,141,214,240,274],"vaccines.":[14],"However,":[15],"this":[16,227],"computational":[17],"task":[18,184],"has":[19,255],"traditionally":[20],"faced":[21],"significant":[22,187],"challenges,":[23,46],"such":[24],"as":[25,266],"scarcity":[27],"structure":[29,83],"data":[30,84],"along":[31],"with":[32],"corresponding":[34],"label":[35],"binding":[38,108],"affinity":[39],"bound":[41],"complexes.":[42],"To":[43],"address":[44],"these":[45],"we":[47,174,215],"introduce":[48],"PepBAN,":[49],"a":[50,76,97,116,183,231,236,242,267],"deep":[51],"learning":[52,92],"framework":[53],"modeling":[55],"PepPI":[56,207],"predictions.":[57],"PepBAN":[58,114,162,229,264],"incorporates":[59],"two":[60],"technical":[61],"advancements:":[62],"(1)":[63],"adopting":[64],"protein":[66,101],"language":[67],"model":[68,79],"ESM-2":[69,74],"to":[70,93,146,190,222],"characterize":[71],"proteins":[72],"or":[75],"graph-based":[77],"foundation":[78],"peptides":[81],"without":[82],"(2)":[86],"leveraging":[87],"conditional":[89],"domain":[90],"adversarial":[91],"enhance":[94],"generalization":[95],"across":[96,168],"broad":[98],"range":[99],"targets,":[102],"especially":[103],"when":[104],"there":[105],"are":[106],"limited":[107],"data.":[109],"At":[110],"core":[112],"bilinear":[117],"attention":[118,155],"network":[119],"(BAN)":[120],"that":[121,161,185],"effectively":[122],"learns":[123],"pattern":[125],"pairwise":[127],"local":[128],"interactions,":[129,140,182],"enables":[130],"identification":[132],"key":[134],"residues":[135,199],"participating":[136],"in":[137,178,245],"offers":[142],"an":[143,217],"intuitive":[144],"approach":[145,221],"interpret":[147],"underlying":[149],"mechanisms":[150],"PepPIs":[152],"via":[153],"analyzing":[154],"weights.":[156],"Our":[157],"numerical":[158],"experiments":[159],"demonstrated":[160,230],"outperformed":[163],"previous":[165],"state-of-the-art":[166],"models":[167,209],"several":[169],"well-established":[170],"benchmark":[171],"studies.":[172],"Furthermore,":[173],"evaluated":[175],"PepBAN's":[176],"applicability":[177],"predicting":[179],"cyclic":[180,224,252],"poses":[186],"challenges":[188],"due":[189],"presence":[192],"noncanonical":[194],"amino":[195],"acids.":[196],"These":[197],"nonstandard":[198],"require":[200],"specialized":[201],"handling,":[202],"which":[203,254],"most":[204],"existing":[205],"sequence-based":[206],"did":[210],"not":[211],"adequately":[212],"address,":[213],"adopt":[216],"atom-resolved":[218],"molecular":[219],"graph":[220],"process":[223],"peptides.":[225],"Despite":[226],"complexity,":[228],"clear":[232],"advantage":[233],"by":[234],"achieving":[235],"superior":[237],"performance":[239],"offering":[241],"distinct":[243],"edge":[244],"tackling":[246],"emerging":[248],"chemical":[249],"space":[250],"peptides,":[253],"great":[256],"potential":[257],"novel":[259],"therapeutic":[260,275],"development.":[261,276],"In":[262],"summary,":[263],"serves":[265],"valuable":[268],"tool":[269],"advancing":[271],"drug":[273]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
