{"id":"https://openalex.org/W7160277929","doi":"https://doi.org/10.48550/arxiv.2605.00948","title":"Co-Generative De Novo Functional Protein Design","display_name":"Co-Generative De Novo Functional Protein Design","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7160277929","doi":"https://doi.org/10.48550/arxiv.2605.00948"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.00948","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.00948","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.00948","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101481014","display_name":"Xinrui Chen","orcid":"https://orcid.org/0000-0001-8780-4076"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Xinrui","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135408305","display_name":"Yizhen Luo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luo, Yizhen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008382543","display_name":"Siqi Fan","orcid":"https://orcid.org/0000-0002-9613-4198"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fan, Siqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5047496977","display_name":"Zaiqing Nie","orcid":"https://orcid.org/0000-0002-1134-2343"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nie, Zaiqing","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5340999960899353,"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":0.5340999960899353,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.15209999680519104,"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":0.06159999966621399,"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/protein-design","display_name":"Protein design","score":0.6039999723434448},{"id":"https://openalex.org/keywords/decodes","display_name":"Decodes","score":0.5479999780654907},{"id":"https://openalex.org/keywords/functional-analysis","display_name":"Functional analysis","score":0.49549999833106995},{"id":"https://openalex.org/keywords/functional-approach","display_name":"Functional approach","score":0.4909000098705292},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4778999984264374},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4404999911785126},{"id":"https://openalex.org/keywords/ambiguity","display_name":"Ambiguity","score":0.40799999237060547},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.4002000093460083},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3747999966144562}],"concepts":[{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.6039999723434448},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5892999768257141},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5702000260353088},{"id":"https://openalex.org/C2778858076","wikidata":"https://www.wikidata.org/wiki/Q5249539","display_name":"Decodes","level":3,"score":0.5479999780654907},{"id":"https://openalex.org/C55112680","wikidata":"https://www.wikidata.org/wiki/Q190549","display_name":"Functional analysis","level":3,"score":0.49549999833106995},{"id":"https://openalex.org/C2777131603","wikidata":"https://www.wikidata.org/wiki/Q5508796","display_name":"Functional approach","level":2,"score":0.4909000098705292},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4778999984264374},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4404999911785126},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.40799999237060547},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.4002000093460083},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3747999966144562},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36899998784065247},{"id":"https://openalex.org/C2988890453","wikidata":"https://www.wikidata.org/wiki/Q5508815","display_name":"Functional diversity","level":2,"score":0.3668000102043152},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.3479999899864197},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3357999920845032},{"id":"https://openalex.org/C64346931","wikidata":"https://www.wikidata.org/wiki/Q4519148","display_name":"Functional design","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C2781089630","wikidata":"https://www.wikidata.org/wiki/Q21856745","display_name":"Realization (probability)","level":2,"score":0.30979999899864197},{"id":"https://openalex.org/C57371142","wikidata":"https://www.wikidata.org/wiki/Q16914225","display_name":"Functional specification","level":5,"score":0.28760001063346863},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.2815999984741211},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.2793000042438507},{"id":"https://openalex.org/C2993410155","wikidata":"https://www.wikidata.org/wiki/Q5508841","display_name":"Functional organization","level":2,"score":0.2777999937534332},{"id":"https://openalex.org/C62235348","wikidata":"https://www.wikidata.org/wiki/Q3264234","display_name":"Functional requirement","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.26840001344680786},{"id":"https://openalex.org/C3675279","wikidata":"https://www.wikidata.org/wiki/Q211935","display_name":"Protein biosynthesis","level":2,"score":0.2653999924659729},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.25519999861717224},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.25220000743865967}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.00948","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.00948","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.00948","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.00948","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"De":[0],"novo":[1,61],"functional":[2,83,88,104,128],"protein":[3,8,56],"design":[4,64],"aims":[5],"to":[6,42,86,106],"generate":[7],"sequences":[9],"that":[10,65,119],"realize":[11],"specified":[12],"biochemical":[13],"functions":[14],"without":[15],"relying":[16],"on":[17],"evolutionary":[18],"templates,":[19],"enabling":[20,73],"broad":[21],"applications":[22],"in":[23,127,132],"biotechnology":[24],"and":[25,45,69,79,130],"medicine.":[26],"Existing":[27],"approaches":[28],"adopt":[29],"either":[30],"direct":[31],"function-to-sequence":[32],"mapping":[33],"or":[34],"decoupled":[35],"structure-sequence":[36],"generation":[37],"strategies":[38],"but":[39],"often":[40],"fail":[41],"achieve":[43],"functionality":[44,78],"foldability":[46,133],"simultaneously.":[47],"To":[48],"address":[49],"this,":[50],"we":[51],"propose":[52],"CodeFP,":[53],"a":[54],"Co-generative":[55],"language":[57],"model":[58],"for":[59],"de":[60],"Functional":[62],"Protein":[63],"simultaneously":[66],"decodes":[67],"sequence":[68],"structure":[70,99],"tokens,":[71,100],"thereby":[72],"superior":[74],"simultaneous":[75],"realization":[76],"of":[77,95,125],"foldability.":[80],"CodeFP":[81,120],"utilizes":[82],"local":[84],"structures":[85],"enrich":[87],"semantic":[89],"encodings,":[90],"overcoming":[91],"the":[92,112,135],"suboptimal":[93],"translation":[94],"flat":[96],"encodings":[97],"into":[98],"while":[101],"introducing":[102],"auxiliary":[103],"supervision":[105],"alleviate":[107],"training":[108],"ambiguity":[109],"stemming":[110],"from":[111],"one-to-many":[113],"structure-to-token":[114],"mapping.":[115],"Extensive":[116],"experiments":[117],"show":[118],"consistently":[121],"achieves":[122],"average":[123],"improvements":[124],"6.1%":[126],"consistency":[129],"3.2%":[131],"over":[134],"strongest":[136],"baseline.":[137]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-05-06T00:00:00"}
