{"id":"https://openalex.org/W4411045445","doi":"https://doi.org/10.1093/bib/bbaf261","title":"Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features","display_name":"Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411045445","doi":"https://doi.org/10.1093/bib/bbaf261","pmid":"https://pubmed.ncbi.nlm.nih.gov/40462515"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf261","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf261","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/bbaf261","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012923763","display_name":"Zehua Sun","orcid":"https://orcid.org/0000-0002-8568-2121"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Zehua Sun","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Department of Materials Science and Engineering, Faculty of Engineering, Monash University , 20 Research Way, New Horizons, Clayton, Victoria 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Department of Materials Science and Engineering, Faculty of Engineering, Monash University , 20 Research Way, New Horizons, Clayton, Victoria 3800 ,","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042066408","display_name":"Jing Xu","orcid":"https://orcid.org/0000-0001-8532-2241"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I4210163881","display_name":"Avenir Health","ror":"https://ror.org/05k833b90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210163881"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Jing Xu","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I4210163881","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100718160","display_name":"Yumeng Zhang","orcid":"https://orcid.org/0000-0002-3194-347X"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I4210135053","display_name":"Quality Research","ror":"https://ror.org/03v0zfc19","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210135053"]},{"id":"https://openalex.org/I4210163881","display_name":"Avenir Health","ror":"https://ror.org/05k833b90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210163881"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Yumeng Zhang","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,","Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,","institution_ids":["https://openalex.org/I4210135053","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I4210163881","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100430651","display_name":"Yiwen Zhang","orcid":"https://orcid.org/0000-0001-9570-4147"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I4210135053","display_name":"Quality Research","ror":"https://ror.org/03v0zfc19","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210135053"]},{"id":"https://openalex.org/I4210163881","display_name":"Avenir Health","ror":"https://ror.org/05k833b90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210163881"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Yiwen Zhang","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,","Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,","institution_ids":["https://openalex.org/I4210135053","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I4210163881","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101627769","display_name":"Zhikang Wang","orcid":"https://orcid.org/0000-0001-9587-1965"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I4210163881","display_name":"Avenir Health","ror":"https://ror.org/05k833b90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210163881"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Zhikang Wang","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I4210163881","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101891945","display_name":"Xiaoyu Wang","orcid":"https://orcid.org/0000-0001-9397-4485"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I4210163881","display_name":"Avenir Health","ror":"https://ror.org/05k833b90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210163881"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Xiaoyu Wang","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I4210163881","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371500","display_name":"Shanshan Li","orcid":"https://orcid.org/0000-0002-9021-8470"},"institutions":[{"id":"https://openalex.org/I4210135053","display_name":"Quality Research","ror":"https://ror.org/03v0zfc19","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210135053"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Shanshan Li","raw_affiliation_strings":["Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,","institution_ids":["https://openalex.org/I4210135053","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100604759","display_name":"Yuming Guo","orcid":"https://orcid.org/0000-0002-1766-6592"},"institutions":[{"id":"https://openalex.org/I4210135053","display_name":"Quality Research","ror":"https://ror.org/03v0zfc19","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210135053"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Yuming Guo","raw_affiliation_strings":["Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University , 553 St Kilda Road, Melbourne, VIC 3004 ,","institution_ids":["https://openalex.org/I4210135053","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091565448","display_name":"Hsin\u2010Hui Shen","orcid":"https://orcid.org/0000-0002-8541-4370"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Hsin Hui Shen","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Department of Materials Science and Engineering, Faculty of Engineering, Monash University , 20 Research Way, New Horizons, Clayton, Victoria 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Department of Materials Science and Engineering, Faculty of Engineering, Monash University , 20 Research Way, New Horizons, Clayton, Victoria 3800 ,","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012709797","display_name":"Jiangning Song","orcid":"https://orcid.org/0000-0001-8031-9086"},"institutions":[{"id":"https://openalex.org/I2799424032","display_name":"Discovery Institute","ror":"https://ror.org/05t8s3y29","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2799424032"]},{"id":"https://openalex.org/I4210163881","display_name":"Avenir Health","ror":"https://ror.org/05k833b90","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210163881"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Jiangning Song","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I2799424032","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Wellington Rd, Clayton, Melbourne, VIC 3800 ,","institution_ids":["https://openalex.org/I4210163881","https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":7.6701,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.97827789,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"26","issue":"3","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":0.9998999834060669,"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":0.9998999834060669,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9977999925613403,"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":0.9957000017166138,"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":0.6202103495597839},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5421100854873657},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5300970673561096},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5161129236221313},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4961908459663391},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.41715508699417114},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4130285382270813},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3301914930343628},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32009899616241455},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21597731113433838},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12189045548439026}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6202103495597839},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5421100854873657},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5300970673561096},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5161129236221313},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4961908459663391},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.41715508699417114},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4130285382270813},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3301914930343628},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32009899616241455},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21597731113433838},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12189045548439026},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf261","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf261","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:40462515","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40462515","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:pubmedcentral.nih.gov:12133682","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12133682","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf261","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf261","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/G7921690166","display_name":null,"funder_award_id":"R01 AI111965","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1583837637","https://openalex.org/W1975304761","https://openalex.org/W1984679573","https://openalex.org/W2015490529","https://openalex.org/W2016023958","https://openalex.org/W2055752079","https://openalex.org/W2067402644","https://openalex.org/W2102461176","https://openalex.org/W2105525514","https://openalex.org/W2108638835","https://openalex.org/W2152380569","https://openalex.org/W2163316049","https://openalex.org/W2165522820","https://openalex.org/W2175270296","https://openalex.org/W2189116376","https://openalex.org/W2339719866","https://openalex.org/W2613333231","https://openalex.org/W2620998958","https://openalex.org/W2791848964","https://openalex.org/W2885195348","https://openalex.org/W2899153547","https://openalex.org/W2914385679","https://openalex.org/W2965128681","https://openalex.org/W2984592028","https://openalex.org/W2984894304","https://openalex.org/W2991176535","https://openalex.org/W2992752586","https://openalex.org/W3025501158","https://openalex.org/W3038004684","https://openalex.org/W3080137602","https://openalex.org/W3081999257","https://openalex.org/W3177828909","https://openalex.org/W3212854871","https://openalex.org/W4205773061","https://openalex.org/W4213430678","https://openalex.org/W4214868967","https://openalex.org/W4281790889","https://openalex.org/W4286251201","https://openalex.org/W4291019815","https://openalex.org/W4291994084","https://openalex.org/W4293649366","https://openalex.org/W4308370073","https://openalex.org/W4309506674","https://openalex.org/W4310253606","https://openalex.org/W4312211520","https://openalex.org/W4313453841","https://openalex.org/W4322754081","https://openalex.org/W4327550249","https://openalex.org/W4366213854","https://openalex.org/W4376478381","https://openalex.org/W4382198814","https://openalex.org/W4384299806","https://openalex.org/W4392162030","https://openalex.org/W4392518459","https://openalex.org/W4396560726","https://openalex.org/W4396873165","https://openalex.org/W4404343420","https://openalex.org/W6667333778"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W4391621807","https://openalex.org/W2611989081","https://openalex.org/W4321487865","https://openalex.org/W4313906399","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W4380075502"],"abstract_inverted_index":{"Antimicrobial":[0],"peptides":[1,5],"(AMPs)":[2],"are":[3,91,111,126],"short":[4],"that":[6,71,153],"play":[7],"critical":[8,166],"roles":[9],"in":[10,174,231],"diverse":[11],"biological":[12],"processes":[13],"and":[14,45,65,101,107,117,123,171,193,198,234],"exhibit":[15],"functional":[16],"activities":[17],"against":[18],"target":[19],"organisms.":[20],"While":[21],"numerous":[22],"methods":[23],"have":[24],"demonstrated":[25],"the":[26,59,139,154,165,184,194,210,216,232],"effectiveness":[27],"of":[28,168,180,187,190,196,209,213,236],"deep":[29],"neural":[30,131,200],"networks":[31,106],"for":[32,218,229],"AMP":[33,78,147,175,221],"identification":[34],"using":[35,128],"sequence":[36,85],"features;":[37],"nevertheless,":[38],"higher-level":[39],"peptide":[40,84,191],"characteristics-such":[41],"as":[42,86],"3D":[43],"structure":[44],"geometric":[46,130,197],"surface":[47,121,172],"features-have":[48],"not":[49],"been":[50],"comprehensively":[51],"explored.":[52],"To":[53],"address":[54],"this":[55,181],"gap,":[56],"we":[57],"introduce":[58],"SSFGM-Model":[60,155,224],"(Sequence,":[61],"Structure,":[62],"Surface,":[63],"Graph,":[64],"Geometric-based":[66],"Model),":[67],"a":[68,87,129,134,205,226],"novel":[69,237],"framework":[70],"integrates":[72],"multiple":[73,188],"feature":[74,135],"types":[75],"to":[76,113,144],"enhance":[77],"identification.":[79,148,176],"The":[80,177,223,240],"model":[81],"represents":[82],"each":[83],"graph,":[88],"where":[89],"nodes":[90],"characterized":[92],"by":[93],"amino":[94],"acid":[95],"features":[96,173],"derived":[97],"from":[98,141],"ProteinBERT,":[99],"ESM-2,":[100],"One-hot":[102],"embeddings.":[103],"Graph":[104],"convolutional":[105],"an":[108],"attention":[109],"mechanism":[110],"employed":[112],"capture":[114],"high-order":[115],"structural":[116],"sequential":[118],"relationships.":[119],"Additionally,":[120],"geometry":[122],"physicochemical":[124],"properties":[125],"processed":[127],"network.":[132],"Finally,":[133],"fusion":[136],"strategy":[137],"combines":[138],"outputs":[140],"these":[142],"subnetworks":[143],"enable":[145],"robust":[146],"Extensive":[149],"benchmarking":[150],"experiments":[151],"demonstrate":[152],"outperforms":[156],"current":[157],"state-of-the-art":[158],"methods.":[159],"An":[160],"ablation":[161],"study":[162],"further":[163],"confirms":[164],"role":[167],"sequence,":[169],"structural,":[170],"key":[178],"contribution":[179],"work":[182],"is":[183,243],"innovative":[185],"integration":[186],"levels":[189],"characteristics":[192],"combination":[195],"graph":[199],"networks.":[201],"This":[202],"approach":[203],"provides":[204],"more":[206,219],"comprehensive":[207],"understanding":[208],"sequence-structure-function":[211],"relationship":[212],"peptides,":[214],"paving":[215],"way":[217],"accurate":[220],"prediction.":[222],"has":[225],"significant":[227],"potential":[228],"applications":[230],"discovery":[233],"design":[235],"AMP-based":[238],"therapeutics.":[239],"source":[241],"code":[242],"publicly":[244],"available":[245],"at":[246],"https://github.com/ggcameronnogg/SSFGM-Model.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}