{"id":"https://openalex.org/W4412825742","doi":"https://doi.org/10.1093/bib/bbaf367","title":"PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids","display_name":"PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412825742","doi":"https://doi.org/10.1093/bib/bbaf367","pmid":"https://pubmed.ncbi.nlm.nih.gov/40748324"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf367","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf367/63918869/bbaf367.pdf","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","license_id":"https://openalex.org/licenses/cc-by","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://academic.oup.com/bib/article-pdf/26/4/bbaf367/63918869/bbaf367.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021422965","display_name":"Ruochi Zhang","orcid":"https://orcid.org/0000-0001-6541-4050"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210145199","display_name":"Guangzhou Research Institute of Synthetic Materials","ror":"https://ror.org/04wgdr728","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145199"]},{"id":"https://openalex.org/I49232843","display_name":"Changchun University","ror":"https://ror.org/02an57k10","country_code":"CN","type":"education","lineage":["https://openalex.org/I49232843"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruochi Zhang","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","School of Artificial Intelligence, Jilin University , Changchun 130012 ,","Syneron Technology , Guangzhou 510700 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University , Changchun 130012 ,","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I49232843"]},{"raw_affiliation_string":"Syneron Technology , Guangzhou 510700 ,","institution_ids":["https://openalex.org/I4210145199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100769821","display_name":"Haoran Wu","orcid":"https://orcid.org/0000-0001-5822-8698"},"institutions":[{"id":"https://openalex.org/I4210145199","display_name":"Guangzhou Research Institute of Synthetic Materials","ror":"https://ror.org/04wgdr728","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoran Wu","raw_affiliation_strings":["Syneron Technology , Guangzhou 510700 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Syneron Technology , Guangzhou 510700 ,","institution_ids":["https://openalex.org/I4210145199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353377","display_name":"Chang Liu","orcid":"https://orcid.org/0000-0003-4959-7541"},"institutions":[{"id":"https://openalex.org/I4210086710","display_name":"Beijing Academy of Social Sciences","ror":"https://ror.org/003ayef58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210086710"]},{"id":"https://openalex.org/I4210162962","display_name":"Beijing Academy of Science and Technology","ror":"https://ror.org/05ct4fn38","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210162962"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chang Liu","raw_affiliation_strings":["Beijing Life Science Academy , Beijing 102209 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Life Science Academy , Beijing 102209 ,","institution_ids":["https://openalex.org/I4210086710","https://openalex.org/I4210162962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009356592","display_name":"Qian Yang","orcid":"https://orcid.org/0000-0002-2170-7086"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Yang","raw_affiliation_strings":["College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I4210134929"]},{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088447454","display_name":"Yuting Xiu","orcid":"https://orcid.org/0009-0005-1859-8674"},"institutions":[{"id":"https://openalex.org/I4210145199","display_name":"Guangzhou Research Institute of Synthetic Materials","ror":"https://ror.org/04wgdr728","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuting Xiu","raw_affiliation_strings":["Syneron Technology , Guangzhou 510700 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Syneron Technology , Guangzhou 510700 ,","institution_ids":["https://openalex.org/I4210145199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102006839","display_name":"Kewei Li","orcid":"https://orcid.org/0000-0002-2797-576X"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kewei Li","raw_affiliation_strings":["College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I4210134929"]},{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100603116","display_name":"Ningning Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210145199","display_name":"Guangzhou Research Institute of Synthetic Materials","ror":"https://ror.org/04wgdr728","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ningning Chen","raw_affiliation_strings":["Syneron Technology , Guangzhou 510700 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Syneron Technology , Guangzhou 510700 ,","institution_ids":["https://openalex.org/I4210145199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100445198","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0002-3526-9494"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]},{"id":"https://openalex.org/I4210145199","display_name":"Guangzhou Research Institute of Synthetic Materials","ror":"https://ror.org/04wgdr728","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145199"]},{"id":"https://openalex.org/I49232843","display_name":"Changchun University","ror":"https://ror.org/02an57k10","country_code":"CN","type":"education","lineage":["https://openalex.org/I49232843"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Wang","raw_affiliation_strings":["College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","School of Artificial Intelligence, Jilin University , Changchun 130012 ,","Syneron Technology , Guangzhou 510700 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I4210134929"]},{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University , Changchun 130012 ,","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I49232843"]},{"raw_affiliation_string":"Syneron Technology , Guangzhou 510700 ,","institution_ids":["https://openalex.org/I4210145199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100322699","display_name":"Yan Wang","orcid":"https://orcid.org/0000-0002-4751-0708"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]},{"id":"https://openalex.org/I4210145199","display_name":"Guangzhou Research Institute of Synthetic Materials","ror":"https://ror.org/04wgdr728","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145199"]},{"id":"https://openalex.org/I49232843","display_name":"Changchun University","ror":"https://ror.org/02an57k10","country_code":"CN","type":"education","lineage":["https://openalex.org/I49232843"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Wang","raw_affiliation_strings":["College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","School of Artificial Intelligence, Jilin University , Changchun 130012 ,","Syneron Technology , Guangzhou 510700 ,"],"raw_orcid":"https://orcid.org/0000-0002-4751-0708","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I4210134929"]},{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University , Changchun 130012 ,","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I49232843"]},{"raw_affiliation_string":"Syneron Technology , Guangzhou 510700 ,","institution_ids":["https://openalex.org/I4210145199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) Thuwal , Thuwal 23955 ,","Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) Thuwal , Thuwal 23955 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST) Thuwal , Thuwal 23955 ,","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) Thuwal , Thuwal 23955 ,","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058786170","display_name":"Fengfeng Zhou","orcid":"https://orcid.org/0000-0002-8108-6007"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fengfeng Zhou","raw_affiliation_strings":["College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,"],"raw_orcid":"https://orcid.org/0000-0002-8108-6007","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I4210134929"]},{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun , Jilin 130012 ,","institution_ids":["https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"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":2.9669,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.91611061,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9997000098228455,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9997000098228455,"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":0.9994000196456909,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9987000226974487,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/non-canonical","display_name":"Non canonical","score":0.8249810934066772},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6027593612670898},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5877305269241333},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5591471195220947},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.48818784952163696},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4639444351196289},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44315019249916077},{"id":"https://openalex.org/keywords/canonical-form","display_name":"Canonical form","score":0.4415930509567261},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3829188346862793},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2750987410545349},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.27327483892440796},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25880151987075806},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2194555699825287},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19193649291992188}],"concepts":[{"id":"https://openalex.org/C3018844941","wikidata":"https://www.wikidata.org/wiki/Q6718887","display_name":"Non canonical","level":2,"score":0.8249810934066772},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6027593612670898},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5877305269241333},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5591471195220947},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.48818784952163696},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4639444351196289},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44315019249916077},{"id":"https://openalex.org/C204707403","wikidata":"https://www.wikidata.org/wiki/Q1152398","display_name":"Canonical form","level":2,"score":0.4415930509567261},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3829188346862793},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2750987410545349},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.27327483892440796},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25880151987075806},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2194555699825287},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19193649291992188},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"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":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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},{"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/bbaf367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf367","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf367/63918869/bbaf367.pdf","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40748324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40748324","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11127915","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12315545","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf367","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf367/63918869/bbaf367.pdf","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","license_id":"https://openalex.org/licenses/cc-by","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/G2058729345","display_name":null,"funder_award_id":"FCC/1/1976-45-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G373900934","display_name":null,"funder_award_id":"REI/1/5404-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5289953175","display_name":null,"funder_award_id":"REI/1/5234-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5348541598","display_name":null,"funder_award_id":"URF/1/4352-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G6661931101","display_name":null,"funder_award_id":"REI/1/5414-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G7618909991","display_name":null,"funder_award_id":"REI/1/5289-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G8253667702","display_name":null,"funder_award_id":"FCC/1/1976-44-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322174","display_name":"People's Government of Jilin Province","ror":"https://ror.org/02fzqav45"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412825742.pdf","grobid_xml":"https://content.openalex.org/works/W4412825742.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1992450378","https://openalex.org/W2022476850","https://openalex.org/W2074995652","https://openalex.org/W2102461176","https://openalex.org/W2121597792","https://openalex.org/W2594502287","https://openalex.org/W2620998958","https://openalex.org/W2739999456","https://openalex.org/W2754194631","https://openalex.org/W2754882069","https://openalex.org/W2796585980","https://openalex.org/W2896811437","https://openalex.org/W2953103783","https://openalex.org/W3037699692","https://openalex.org/W3094309150","https://openalex.org/W3146944767","https://openalex.org/W3161725201","https://openalex.org/W3199607358","https://openalex.org/W4205773061","https://openalex.org/W4206642145","https://openalex.org/W4302008537","https://openalex.org/W4327550249","https://openalex.org/W4327694659","https://openalex.org/W4362657509","https://openalex.org/W4382319456","https://openalex.org/W4387860362","https://openalex.org/W4387865628","https://openalex.org/W4391440627","https://openalex.org/W6779909149","https://openalex.org/W6784741312","https://openalex.org/W6838894335","https://openalex.org/W6845259520","https://openalex.org/W6854480846"],"related_works":["https://openalex.org/W1955343808","https://openalex.org/W4253496423","https://openalex.org/W2900905684","https://openalex.org/W2023560604","https://openalex.org/W2158768090","https://openalex.org/W2041084450","https://openalex.org/W2058782399","https://openalex.org/W2125521041","https://openalex.org/W1972101047","https://openalex.org/W3093255180"],"abstract_inverted_index":{"The":[0],"recent":[1],"interest":[2],"in":[3,39,53,120,143,164],"peptides":[4,28,148],"incorporating":[5],"non-canonical":[6,27,94,153],"amino":[7,95,154],"acids":[8],"has":[9],"surged":[10],"within":[11],"the":[12,54,83,108,171],"scientific":[13],"community,":[14],"driven":[15],"by":[16],"their":[17,46],"enhanced":[18],"stability":[19],"and":[20,36,42,86,93,132,152,156,175],"resistance":[21],"to":[22,106],"proteolytic":[23],"degradation.":[24],"These":[25,136],"so-called":[26],"offer":[29],"significant":[30],"potential":[31],"for":[32,82,161],"modifying":[33],"biological,":[34],"pharmacological,":[35],"physiochemical":[37],"characteristics":[38],"both":[40,91,150],"native":[41],"synthetic":[43],"contexts.":[44],"Despite":[45],"advantages,":[47],"there":[48],"remains":[49],"a":[50,77,99,121,158],"notable":[51],"gap":[52],"availability":[55],"of":[56,62,88,112,123,147],"an":[57],"efficient":[58],"pre-trained":[59],"model":[60],"capable":[61],"effectively":[63],"capturing":[64],"feature":[65],"representations":[66,111,146],"from":[67],"such":[68],"intricate":[69],"peptide":[70,124],"sequences.":[71],"This":[72],"study":[73],"herein":[74],"introduces":[75],"PepLand,":[76],"novel":[78],"pre-training":[79],"framework":[80],"designed":[81],"comprehensive":[84],"representation":[85],"analysis":[87],"peptides,":[89],"encompassing":[90],"canonical":[92,151],"acids.":[96],"PepLand":[97],"leverages":[98],"general-purpose":[100],"multi-view":[101],"heterogeneous":[102],"graph":[103],"neural":[104],"network":[105],"unveil":[107],"subtle":[109],"structural":[110],"peptides.":[113],"Our":[114],"empirical":[115],"evaluations":[116],"demonstrate":[117],"PepLand's":[118,140],"proficiency":[119],"range":[122],"property":[125],"prediction":[126],"tasks,":[127],"including":[128],"cell":[129],"penetrability,":[130],"solubility,":[131],"protein-peptide":[133],"binding":[134],"affinity.":[135],"rigorous":[137],"assessments":[138],"affirm":[139],"superior":[141],"capability":[142],"discerning":[144],"critical":[145],"with":[149],"acids,":[155],"provide":[157],"robust":[159],"foundation":[160],"transformative":[162],"advances":[163],"peptide-focused":[165],"pharmaceutical":[166],"research.":[167],"We":[168],"have":[169],"made":[170],"entire":[172],"source":[173],"code":[174],"datasets":[176],"available":[177],"at":[178],"http://www.healthinformaticslab.org/supp/resources.php":[179],"or":[180],"https://github.com/zhangruochi/PepLand.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
