{"id":"https://openalex.org/W4410074675","doi":"https://doi.org/10.1101/2025.04.29.651236","title":"nanoFOLD : sequence design of nanobodies via inverse folding","display_name":"nanoFOLD : sequence design of nanobodies via inverse folding","publication_year":2025,"publication_date":"2025-05-03","ids":{"openalex":"https://openalex.org/W4410074675","doi":"https://doi.org/10.1101/2025.04.29.651236"},"language":"en","primary_location":{"id":"doi:10.1101/2025.04.29.651236","doi":"https://doi.org/10.1101/2025.04.29.651236","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.29.651236","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/03/2025.04.29.651236.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/03/2025.04.29.651236.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092422087","display_name":"Dawid Chomicz","orcid":"https://orcid.org/0009-0000-7943-6082","observed_orcids":["https://orcid.org/0009-0000-7943-6082"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dawid Chomicz","raw_affiliation_strings":["NaturalAntibody, Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody, Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072822527","display_name":"Bartosz Janusz","orcid":"https://orcid.org/0000-0001-6448-0451","observed_orcids":["https://orcid.org/0000-0001-6448-0451"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bartosz Janusz","raw_affiliation_strings":["NaturalAntibody, Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody, Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sonia Wrobel","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sonia Wrobel","raw_affiliation_strings":["NaturalAntibody, Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody, Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009007983","display_name":"Pawe\u0142 Dudzic","orcid":"https://orcid.org/0009-0006-3849-7640","observed_orcids":["https://orcid.org/0009-0006-3849-7640"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pawel Dudzic","raw_affiliation_strings":["NaturalAntibody, Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody, Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073238401","display_name":"Adithya Polasa","orcid":"https://orcid.org/0000-0002-7764-6585","observed_orcids":["https://orcid.org/0000-0002-7764-6585"]},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adithya Polasa","raw_affiliation_strings":["Boehringer-Ingelheim, Ridgefield, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boehringer-Ingelheim, Ridgefield, CT, USA","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071320323","display_name":"Kyle Martin","orcid":"https://orcid.org/0000-0001-6946-4813","observed_orcids":["https://orcid.org/0000-0001-6946-4813"]},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle Martin","raw_affiliation_strings":["Boehringer-Ingelheim, Ridgefield, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boehringer-Ingelheim, Ridgefield, CT, USA","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062354324","display_name":"Steven J. Darnell","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Darnell","raw_affiliation_strings":["Boehringer-Ingelheim, Ridgefield, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boehringer-Ingelheim, Ridgefield, CT, USA","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038298924","display_name":"Stephen R. Comeau","orcid":"https://orcid.org/0000-0003-4281-2026","observed_orcids":["https://orcid.org/0000-0003-4281-2026"]},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen R. Comeau","raw_affiliation_strings":["Boehringer-Ingelheim, Ridgefield, CT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boehringer-Ingelheim, Ridgefield, CT, USA","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015244397","display_name":"Konrad Krawczyk","orcid":"https://orcid.org/0000-0003-0697-5522","observed_orcids":["https://orcid.org/0000-0003-0697-5522"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Konrad Krawczyk","raw_affiliation_strings":["NaturalAntibody, Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody, Szczecin, Poland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5015244397"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"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":0.7231000065803528,"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":0.7231000065803528,"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":0.20499999821186066,"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"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.021800000220537186,"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/nanobodies","display_name":"nanobodies","score":0.9549999833106995},{"id":"https://openalex.org/keywords/inverse-folding","display_name":"inverse folding","score":0.9800000190734863},{"id":"https://openalex.org/keywords/sequence-design","display_name":"sequence design","score":0.8669999837875366},{"id":"https://openalex.org/keywords/antibody-engineering","display_name":"antibody engineering","score":0.6809999942779541},{"id":"https://openalex.org/keywords/next-generation-sequencing","display_name":"next-generation sequencing","score":0.7059999704360962},{"id":"https://openalex.org/keywords/biological-therapy","display_name":"biologic therapy","score":0.7319999933242798},{"id":"https://openalex.org/keywords/computational-protein-design","display_name":"computational protein design","score":0.6190000176429749}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.7145564556121826},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.6255366206169128},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5798449516296387},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3442440629005432},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3365671634674072},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32103270292282104},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23605450987815857},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17788490653038025},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.13323360681533813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12273097038269043},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08729445934295654},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.05025777220726013}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2025.04.29.651236","doi":"https://doi.org/10.1101/2025.04.29.651236","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.29.651236","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/03/2025.04.29.651236.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2025.04.29.651236","doi":"https://doi.org/10.1101/2025.04.29.651236","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.29.651236","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/03/2025.04.29.651236.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410074675.pdf","grobid_xml":"https://content.openalex.org/works/W4410074675.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W2110505462","https://openalex.org/W2560647685","https://openalex.org/W2950118240","https://openalex.org/W2980681402","https://openalex.org/W3156522942","https://openalex.org/W3179485843","https://openalex.org/W3206187363","https://openalex.org/W3214417031","https://openalex.org/W4221053240","https://openalex.org/W4225008297","https://openalex.org/W4285386587","https://openalex.org/W4291165742","https://openalex.org/W4296032638","https://openalex.org/W4353090737","https://openalex.org/W4366823175","https://openalex.org/W4378714914","https://openalex.org/W4388093546","https://openalex.org/W4390880595","https://openalex.org/W4390892405","https://openalex.org/W4392563999","https://openalex.org/W4393044531","https://openalex.org/W4396721167","https://openalex.org/W4399052323","https://openalex.org/W4400313991","https://openalex.org/W4403329018","https://openalex.org/W4415795751","https://openalex.org/W4415929062","https://openalex.org/W7133248214"],"related_works":["https://openalex.org/W7139969690","https://openalex.org/W4396787690","https://openalex.org/W4408763951","https://openalex.org/W4388093546","https://openalex.org/W7096422076","https://openalex.org/W7211942594","https://openalex.org/W6925195064","https://openalex.org/W7163805212","https://openalex.org/W7169871304","https://openalex.org/W7159609429"],"abstract_inverted_index":{"Abstract":[0],"Antibodies":[1],"devoid":[2],"of":[3,10,30,71],"light":[4],"chains":[5],"are":[6,18],"a":[7,41],"promising":[8],"class":[9],"biotherapeutics.":[11],"Computational":[12],"methods":[13],"that":[14],"address":[15],"these":[16],"molecules":[17],"crucially":[19],"needed":[20],"to":[21,39,62],"accelerate":[22],"the":[23],"traditional,":[24],"long":[25],"and":[26,78],"expensive":[27],"experimental":[28],"process":[29],"their":[31],"discovery.":[32],"Inverse":[33],"folding,":[34],"wherein":[35],"one":[36],"is":[37,46],"tasked":[38],"predict":[40],"sequence":[42],"given":[43],"molecular":[44],"coordinates,":[45],"an":[47,57],"established":[48],"method":[49,60],"in":[50,68],"scaffold-based":[51],"protein":[52],"design.":[53,81],"Here":[54],"we":[55],"develop":[56],"inverse":[58],"folding":[59],"speci\ufb01c":[61],"nanobodies.":[63],"We":[64],"demonstrate":[65],"its":[66],"application":[67],"nanobody-engineering":[69],"scenarios":[70],"enriching":[72],"binders":[73],"from":[74],"next-generation":[75],"sequencing":[76],"experiments":[77],"novel":[79],"binder":[80]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2025-05-05T00:00:00"}
