{"id":"https://openalex.org/W7165018224","doi":"https://doi.org/10.48550/arxiv.2606.17127","title":"Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3","display_name":"Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3","publication_year":2026,"publication_date":"2026-06-15","ids":{"openalex":"https://openalex.org/W7165018224","doi":"https://doi.org/10.48550/arxiv.2606.17127"},"language":"en","primary_location":{"id":"pmh:oai:pubmedcentral.nih.gov:13308455","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13308455/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13308455/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5134221010","display_name":"Jay Jung","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jung, Jay","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138798326","display_name":"Xiaohan Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Xiaohan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138787106","display_name":"Shenghan Song","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Song, Shenghan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138815004","display_name":"Mahmoud Sayedahmed","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sayedahmed, Mahmoud","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138775124","display_name":"Chijian Xiang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiang, Chijian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138787327","display_name":"Yunong Xu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Yunong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138824846","display_name":"Ahmed AbdelKhalek","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"AbdelKhalek, Ahmed","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135302649","display_name":"Severin T. Schneebeli","orcid":"https://orcid.org/0000-0002-9511-9922"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schneebeli, Severin T.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017951504","display_name":"Matthew J. Wargo","orcid":"https://orcid.org/0000-0001-5659-749X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wargo, Matthew J.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138820951","display_name":"Jianing Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Jianing","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5138824773","display_name":"Safwan Wshah","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wshah, Safwan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9223999977111816,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9223999977111816,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.015300000086426735,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.015300000086426735,"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/generative-grammar","display_name":"Generative grammar","score":0.6869999766349792},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.5706999897956848},{"id":"https://openalex.org/keywords/antimicrobial-peptides","display_name":"Antimicrobial peptides","score":0.5490999817848206},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5271000266075134},{"id":"https://openalex.org/keywords/antimicrobial","display_name":"Antimicrobial","score":0.491100013256073},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.39250001311302185},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.38429999351501465},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.36070001125335693}],"concepts":[{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.6869999766349792},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.5706999897956848},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5565999746322632},{"id":"https://openalex.org/C540938839","wikidata":"https://www.wikidata.org/wiki/Q1201508","display_name":"Antimicrobial peptides","level":3,"score":0.5490999817848206},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5271000266075134},{"id":"https://openalex.org/C4937899","wikidata":"https://www.wikidata.org/wiki/Q68541106","display_name":"Antimicrobial","level":2,"score":0.491100013256073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4251999855041504},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4099000096321106},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39329999685287476},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.39250001311302185},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.38429999351501465},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.36070001125335693},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3255000114440918},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.32350000739097595},{"id":"https://openalex.org/C2107291","wikidata":"https://www.wikidata.org/wiki/Q14886885","display_name":"Mediator","level":2,"score":0.3174000084400177},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.31040000915527344},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.29989999532699585},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2980000078678131},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29420000314712524},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.29019999504089355},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2896000146865845},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.28110000491142273},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.2786000072956085},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.2768999934196472},{"id":"https://openalex.org/C132141352","wikidata":"https://www.wikidata.org/wiki/Q1724806","display_name":"Lantibiotics","level":4,"score":0.2766999900341034},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.266400009393692},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.2574999928474426},{"id":"https://openalex.org/C202751555","wikidata":"https://www.wikidata.org/wiki/Q221681","display_name":"In vitro","level":2,"score":0.25}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:pubmedcentral.nih.gov:13308455","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13308455/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2606.17127","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.17127","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:13308455","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13308455/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.6489130258560181}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Antimicrobial":[0,9],"resistance":[1],"causes":[2],"to":[3,24,54],"over":[4],"a":[5,13,45,123,132,159],"million":[6],"deaths":[7],"annually.":[8],"peptides":[10,26],"(AMPs)":[11],"are":[12,20,35],"promising":[14],"solution,":[15],"but":[16,161],"generative":[17,52,82,165],"AMP":[18,83,128],"models":[19,84],"not":[21],"yet":[22],"ready":[23],"design":[25],"with":[27,104,147],"non-natural":[28],"amino":[29],"acids":[30,56],"and/or":[31],"chemical":[32],"modifications,":[33],"which":[34,131],"essential":[36],"for":[37,126,138],"real-world":[38],"peptide":[39,172],"drugs.":[40],"We":[41,88],"present":[42,121],"AMPGAN":[43,73],"v3,":[44],"multi-objective":[46],"conditional":[47],"GAN":[48],"that":[49],"expands":[50],"the":[51,105],"vocabulary":[53],"D-amino":[55],"and":[57,66,79,141,166],"N/C-terminus":[58],"modifications":[59],"such":[60],"as":[61],"amidation.":[62],"By":[63],"separating":[64],"adversarial":[65],"activity-aware":[67],"supervision":[68],"across":[69],"two":[70,98],"specialized":[71,136],"discriminators,":[72],"v3":[74],"substantially":[75],"improves":[76],"training":[77],"stability":[78],"outperforms":[80],"prior":[81],"on":[85,158],"external":[86],"classifiers.":[87],"validated":[89],"five":[90],"candidates":[91],"spanning":[92],"three":[93],"structural":[94],"classes":[95],"in":[96,130,149,170],"vitro;":[97],"showed":[99],"activity":[100],"against":[101,112],"Gram-positive":[102],"strains,":[103],"best":[106],"candidate":[107],"reaching":[108],"MIC":[109],"8":[110],"\u03bcg/mL":[111],"B.":[113],"subtilis.":[114],"To":[115],"support":[116],"downstream":[117],"curation,":[118],"we":[119],"further":[120],"PepCraft,":[122],"multi-agent":[124],"framework":[125],"end-to-end":[127],"discovery":[129],"Planning":[133],"Agent":[134],"orchestrates":[135],"executors":[137],"generation,":[139],"filtering,":[140],"verification.":[142],"Its":[143],"prioritization":[144],"recommendations":[145],"align":[146],"our":[148],"vitro":[150],"outcomes.":[151],"Together,":[152],"these":[153],"contributions":[154],"let":[155],"us":[156],"examine,":[157],"small":[160],"real":[162],"scale,":[163],"how":[164],"agentic":[167],"AI":[168],"compose":[169],"therapeutic":[171],"discovery.":[173],"Code:":[174],"https://github.com/marszzibros/AMPGANv3":[175]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2026-06-18T00:00:00"}
