{"id":"https://openalex.org/W7138343675","doi":"https://doi.org/10.1609/aaai.v40i1.37037","title":"DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design","display_name":"DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design","publication_year":2026,"publication_date":"2026-03-14","ids":{"openalex":"https://openalex.org/W7138343675","doi":"https://doi.org/10.1609/aaai.v40i1.37037"},"language":null,"primary_location":{"id":"doi:10.1609/aaai.v40i1.37037","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i1.37037","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1609/aaai.v40i1.37037","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5129746909","display_name":"Yanting Li","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanting Li","raw_affiliation_strings":["The Chinese University of Hong Kong","The Chinese University of Hong Kong\nHong Kong University of Science and Technology (Guangzhou)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"The Chinese University of Hong Kong\nHong Kong University of Science and Technology (Guangzhou)","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129649906","display_name":"Zikang Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zikang Wang","raw_affiliation_strings":["The Hong Kong Polytechnic University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Hong Kong Polytechnic University","institution_ids":["https://openalex.org/I14243506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038913434","display_name":"Jiyue Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiyue Jiang","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129698668","display_name":"Ziqian Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ziqian Lin","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045822520","display_name":"Dongchen He","orcid":"https://orcid.org/0009-0004-4400-1133"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Dongchen He","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129681998","display_name":"Yuheng Shan","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yuheng Shan","raw_affiliation_strings":["National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yanruisheng Shao","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanruisheng Shao","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129740825","display_name":"Jiayi Li","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiayi Li","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129657483","display_name":"Xiangyu Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Xiangyu Shi","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078001917","display_name":"Jiuming Wang","orcid":"https://orcid.org/0009-0003-9591-156X"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiuming Wang","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129655968","display_name":"Yanyu Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanyu Chen","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129721560","display_name":"Yimin Fan","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yimin Fan","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129714142","display_name":"Han Li","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Han Li","raw_affiliation_strings":["The Chinese University of Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129728395","display_name":"Yu Li","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yu Li","raw_affiliation_strings":["The Chinese University of Hong Kong","The Chinese University of Hong Kong\nHong Kong University of Science and Technology (Guangzhou)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"The Chinese University of Hong Kong\nHong Kong University of Science and Technology (Guangzhou)","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"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":"40","issue":"1","first_page":"712","last_page":"720"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8054999709129333,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.8054999709129333,"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":0.06040000170469284,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.035599999129772186,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.6656000018119812},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.5340999960899353},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.5304999947547913},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5145999789237976},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.44699999690055847},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.43529999256134033},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.41690000891685486},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.41440001130104065}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6656000018119812},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6237999796867371},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.564300000667572},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5340999960899353},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5304999947547913},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5145999789237976},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.44699999690055847},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.43529999256134033},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.41690000891685486},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.41440001130104065},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.40130001306533813},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38040000200271606},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36880001425743103},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.34220001101493835},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.32899999618530273},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.30489999055862427},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.2824999988079071},{"id":"https://openalex.org/C104065381","wikidata":"https://www.wikidata.org/wiki/Q1002535","display_name":"Geometric modeling","level":2,"score":0.2752000093460083},{"id":"https://openalex.org/C108882727","wikidata":"https://www.wikidata.org/wiki/Q2991685","display_name":"Solid modeling","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2597000002861023},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.25270000100135803},{"id":"https://openalex.org/C7305733","wikidata":"https://www.wikidata.org/wiki/Q207961","display_name":"Geometric shape","level":2,"score":0.2502000033855438}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1609/aaai.v40i1.37037","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i1.37037","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1609/aaai.v40i1.37037","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i1.37037","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Inverse":[0],"Protein":[1],"Folding":[2],"(IPF)":[3],"is":[4,112],"a":[5,25,77,107,161],"critical":[6],"subtask":[7],"in":[8,36,151,157],"the":[9,59,131,136,144],"field":[10],"of":[11,21,141,147,163],"protein":[12,84,152],"design,":[13,85],"aiming":[14],"to":[15,56,114],"engineer":[16],"amino":[17],"acid":[18],"sequences":[19,121],"capable":[20],"folding":[22],"correctly":[23],"into":[24,106],"specified":[26],"three-dimensional":[27],"(3D)":[28],"conformation.":[29],"Although":[30],"substantial":[31],"progress":[32],"has":[33],"been":[34],"achieved":[35],"recent":[37],"years,":[38],"existing":[39],"methods":[40],"generally":[41],"rely":[42],"on":[43],"either":[44],"backbone":[45,89,96],"coordinates":[46,97],"or":[47],"molecular":[48],"surface":[49,101],"features":[50],"alone,":[51],"which":[52,86],"restricts":[53],"their":[54],"ability":[55],"fully":[57],"capture":[58],"complex":[60],"chemical":[61,102],"and":[62,91,103,118,126,169],"geometric":[63,104],"constraints":[64],"necessary":[65],"for":[66,82],"precise":[67],"sequence":[68],"prediction.":[69],"To":[70],"address":[71],"this":[72],"limitation,":[73],"we":[74],"present":[75],"DS-ProGen,":[76],"dual-structure":[78],"deep":[79],"language":[80],"model":[81],"functional":[83,174],"integrates":[87],"both":[88,124],"geometry":[90],"surface-level":[92],"representations.":[93],"By":[94],"incorporating":[95],"as":[98,100],"well":[99],"descriptors":[105],"next-amino-acid":[108],"prediction":[109],"paradigm,":[110],"DS-ProGen":[111,134,155],"able":[113],"generate":[115],"functionally":[116],"relevant":[117],"structurally":[119],"stable":[120],"while":[122],"satisfying":[123],"global":[125],"local":[127],"conformational":[128],"constraints.":[129],"On":[130],"PRIDE":[132],"dataset,":[133],"attains":[135],"current":[137],"state-of-the-art":[138],"recovery":[139],"rate":[140],"61.47%,":[142],"demonstrating":[143],"synergistic":[145],"advantage":[146],"multi-modal":[148],"structural":[149],"encoding":[150],"design.":[153],"Furthermore,":[154],"excels":[156],"predicting":[158],"interactions":[159],"with":[160],"variety":[162],"biological":[164],"partners,":[165],"including":[166],"ligands,":[167],"ions,":[168],"RNA,":[170],"confirming":[171],"its":[172],"robust":[173],"retention":[175],"capabilities.":[176]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2026-03-18T00:00:00"}
