{"id":"https://openalex.org/W7160383164","doi":"https://doi.org/10.48550/arxiv.2605.03360","title":"A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion","display_name":"A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion","publication_year":2026,"publication_date":"2026-05-05","ids":{"openalex":"https://openalex.org/W7160383164","doi":"https://doi.org/10.48550/arxiv.2605.03360"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.03360","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.03360","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":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.03360","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5135434868","display_name":"Chaoran Cheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cheng, Chaoran","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135522646","display_name":"Jiaqi Guan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guan, Jiaqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113211784","display_name":"Milong Ren","orcid":"https://orcid.org/0009-0008-5245-246X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ren, Milong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135453994","display_name":"Chengyue Gong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gong, Chengyue","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135508530","display_name":"Cong Liu","orcid":"https://orcid.org/0000-0002-8057-8552"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Cong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135419718","display_name":"Xinshi Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Xinshi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135532194","display_name":"Ge Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Ge","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5000123315","display_name":"Wenzhi Xiao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiao, Wenzhi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4787999987602234,"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":0.4787999987602234,"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":0.2630999982357025,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.02630000002682209,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cascade","display_name":"Cascade","score":0.5066999793052673},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.49570000171661377},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.48010000586509705},{"id":"https://openalex.org/keywords/atomic-model","display_name":"Atomic model","score":0.4666000008583069},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.4214000105857849},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41359999775886536},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.36090001463890076},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.34790000319480896}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5942000150680542},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.5066999793052673},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.49570000171661377},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.48010000586509705},{"id":"https://openalex.org/C194778546","wikidata":"https://www.wikidata.org/wiki/Q15308119","display_name":"Atomic model","level":2,"score":0.4666000008583069},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4611000120639801},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.4214000105857849},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41359999775886536},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3961000144481659},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.36090001463890076},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.357699990272522},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.34790000319480896},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34769999980926514},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3375999927520752},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3361999988555908},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.31439998745918274},{"id":"https://openalex.org/C45493050","wikidata":"https://www.wikidata.org/wiki/Q7884934","display_name":"Unified Model","level":2,"score":0.30799999833106995},{"id":"https://openalex.org/C38111792","wikidata":"https://www.wikidata.org/wiki/Q15712714","display_name":"Biomolecular structure","level":3,"score":0.2939000129699707},{"id":"https://openalex.org/C200902554","wikidata":"https://www.wikidata.org/wiki/Q4817332","display_name":"Atomic diffusion","level":2,"score":0.2870999872684479},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.28110000491142273},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26080000400543213},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.25929999351501465},{"id":"https://openalex.org/C123122884","wikidata":"https://www.wikidata.org/wiki/Q371730","display_name":"Well-defined","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.25600001215934753},{"id":"https://openalex.org/C2993467848","wikidata":"https://www.wikidata.org/wiki/Q901147","display_name":"Atomic charge","level":3,"score":0.2522999942302704}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.03360","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.03360","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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.03360","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.03360","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":"Preprint"},"sustainable_development_goals":[{"display_name":"Life below water","id":"https://metadata.un.org/sdg/14","score":0.6283881068229675}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"We":[0],"present":[1],"A-CODE,":[2],"a":[3,40,99,134],"fully":[4,37,130],"atomic":[5,38,114,131],"unified":[6,41],"one-stage":[7,72,95],"protein":[8,67],"co-design":[9,96],"model":[10],"that":[11,25,142],"simultaneously":[12],"refines":[13],"discrete":[14],"atom":[15,19],"types":[16],"and":[17,73,82],"continuous":[18],"coordinates.":[20],"Unlike":[21],"predominant":[22],"two-stage":[23,74,87],"methods":[24],"cascade":[26],"structure":[27],"design":[28,75,88],"with":[29,92],"amino":[30,125],"acid-level":[31],"sequence":[32],"design,":[33,79],"our":[34,113],"approach":[35],"is":[36],"within":[39],"multimodal":[42],"diffusion":[43],"framework,":[44],"in":[45,103],"which":[46],"residue":[47],"identities":[48],"are":[49],"inferred":[50],"solely":[51],"from":[52],"atom-level":[53],"predictions.":[54],"Built":[55],"upon":[56],"the":[57,93,118],"powerful":[58],"all-atom":[59,139],"architecture,":[60],"A-CODE":[61,80],"achieves":[62,98],"superior":[63],"designability":[64],"for":[65,117,138],"unconditional":[66],"generation,":[68],"outperforming":[69],"all":[70],"existing":[71,85,94],"models.":[76],"For":[77],"binder":[78],"rivals":[81],"even":[83],"outperforms":[84],"state-of-the-art":[86],"models":[89],"and,":[90],"compared":[91],"model,":[97],"drastic":[100],"tenfold":[101],"improvement":[102],"success":[104],"rate":[105],"on":[106],"hard":[107],"tasks.":[108],"The":[109],"inherent":[110],"flexibility":[111],"of":[112],"formulation":[115],"enables,":[116],"first":[119],"time,":[120],"seamless":[121],"adaptation":[122],"to":[123,147],"non-canonical":[124],"acid":[126],"(ncAA)":[127],"modeling.":[128],"Our":[129],"framework":[132],"establishes":[133],"new,":[135],"versatile":[136],"foundation":[137],"generative":[140],"modeling":[141],"can":[143],"be":[144],"naturally":[145],"extended":[146],"complex":[148],"biomolecular":[149],"systems.":[150]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-07T00:00:00"}
