{"id":"https://openalex.org/W4413043632","doi":"https://doi.org/10.1186/s13321-025-01069-2","title":"Nanodesigner: resolving the complex-CDR interdependency with iterative refinement","display_name":"Nanodesigner: resolving the complex-CDR interdependency with iterative refinement","publication_year":2025,"publication_date":"2025-08-07","ids":{"openalex":"https://openalex.org/W4413043632","doi":"https://doi.org/10.1186/s13321-025-01069-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/40775723"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01069-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01069-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01069-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01069-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116472738","display_name":"Melissa Maria Rios Zertuche","orcid":null},"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":true,"raw_author_name":"Melissa Maria Rios Zertuche","raw_affiliation_strings":["Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069397549","display_name":"\u015eenay Kafkas","orcid":"https://orcid.org/0000-0001-7509-5786"},"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":"\u015eenay Kafkas","raw_affiliation_strings":["KAUST Beacon Development, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"KAUST Beacon Development, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003503388","display_name":"Dominik Renn","orcid":"https://orcid.org/0000-0002-6171-2955"},"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":"Dominik Renn","raw_affiliation_strings":["KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071153001","display_name":"Magnus Rueping","orcid":"https://orcid.org/0000-0003-4580-5227"},"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"]},{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE","SA"],"is_corresponding":false,"raw_author_name":"Magnus Rueping","raw_affiliation_strings":["Institute for Experimental Molecular Imaging (ExMI), University Clinic, RWTH Aachen, Forckenbeckstra\u00dfe 55, 52074, Aachen, Germany","KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","KAUST Center of Excellence for Generative AI, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Institute for Experimental Molecular Imaging (ExMI), University Clinic, RWTH Aachen, Forckenbeckstra\u00dfe 55, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"KAUST Center of Excellence for Generative AI, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043808311","display_name":"Robert Hoehndorf","orcid":"https://orcid.org/0000-0001-8149-5890"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert Hoehndorf","raw_affiliation_strings":["Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","KAUST Center of Excellence for Generative AI, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","SDAIA-KAUST Center of Excellence in Data Science and Artificial Intelligence, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa"],"affiliations":[{"raw_affiliation_string":"Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","institution_ids":[]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","institution_ids":[]},{"raw_affiliation_string":"KAUST Center of Excellence for Generative AI, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","institution_ids":[]},{"raw_affiliation_string":"KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","institution_ids":[]},{"raw_affiliation_string":"SDAIA-KAUST Center of Excellence in Data Science and Artificial Intelligence, King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. robert.hoehndorf@kaust.edu.sa","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5116472738"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1734599,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"120","last_page":"120"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10558","display_name":"Advancements in Semiconductor Devices and Circuit Design","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10558","display_name":"Advancements in Semiconductor Devices and Circuit Design","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11255","display_name":"Microfluidic and Bio-sensing Technologies","score":0.9835000038146973,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10472","display_name":"Semiconductor materials and devices","score":0.9718999862670898,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7347047328948975},{"id":"https://openalex.org/keywords/interdependence","display_name":"Interdependence","score":0.6180141568183899},{"id":"https://openalex.org/keywords/iterative-refinement","display_name":"Iterative refinement","score":0.4782258868217468},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42259421944618225},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38256126642227173},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.30639588832855225}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7347047328948975},{"id":"https://openalex.org/C185874996","wikidata":"https://www.wikidata.org/wiki/Q269699","display_name":"Interdependence","level":2,"score":0.6180141568183899},{"id":"https://openalex.org/C2779982483","wikidata":"https://www.wikidata.org/wiki/Q6094420","display_name":"Iterative refinement","level":2,"score":0.4782258868217468},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42259421944618225},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38256126642227173},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30639588832855225},{"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":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01069-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01069-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01069-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40775723","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40775723","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:75525dff57c54d31a2d5bcad19b41197","is_oa":true,"landing_page_url":"https://doaj.org/article/75525dff57c54d31a2d5bcad19b41197","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-11 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12333243","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12333243","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01069-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01069-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01069-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G3154415231","display_name":null,"funder_award_id":"URF/1/4697-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5380366079","display_name":null,"funder_award_id":"URF/1/5041-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G7384501959","display_name":null,"funder_award_id":"REI/1/5235-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G7444020395","display_name":null,"funder_award_id":"URF/1/4675-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413043632.pdf","grobid_xml":"https://content.openalex.org/works/W4413043632.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1956208665","https://openalex.org/W1985743545","https://openalex.org/W2023490488","https://openalex.org/W2049633694","https://openalex.org/W2105273832","https://openalex.org/W2110505462","https://openalex.org/W2119475170","https://openalex.org/W2136567909","https://openalex.org/W2140673705","https://openalex.org/W2160415526","https://openalex.org/W2161151688","https://openalex.org/W2246074199","https://openalex.org/W2508425869","https://openalex.org/W2914298720","https://openalex.org/W2949223833","https://openalex.org/W2950954328","https://openalex.org/W2953176058","https://openalex.org/W2980681402","https://openalex.org/W2993866869","https://openalex.org/W2999958881","https://openalex.org/W3015438624","https://openalex.org/W3088573183","https://openalex.org/W3135044423","https://openalex.org/W3207815566","https://openalex.org/W4206280288","https://openalex.org/W4210325440","https://openalex.org/W4225604225","https://openalex.org/W4225693775","https://openalex.org/W4288065659","https://openalex.org/W4312198153","https://openalex.org/W4353090737","https://openalex.org/W4366998330","https://openalex.org/W4384695412","https://openalex.org/W4392968035","https://openalex.org/W4396721167","https://openalex.org/W4399869197","https://openalex.org/W6600129504","https://openalex.org/W6600168703","https://openalex.org/W6733130978","https://openalex.org/W6814580796"],"related_works":["https://openalex.org/W2139079562","https://openalex.org/W2749324135","https://openalex.org/W2051487156","https://openalex.org/W2908433117","https://openalex.org/W2073681303","https://openalex.org/W2969604939","https://openalex.org/W2378306841","https://openalex.org/W114687057","https://openalex.org/W3122988618","https://openalex.org/W1994631104"],"abstract_inverted_index":{"Camelid":[0],"heavy-chain":[1],"only":[2],"antibodies":[3],"consist":[4],"of":[5,47,137,160,168],"two":[6],"heavy":[7],"chains":[8],"and":[9,44,69,95,110,170],"single":[10],"variable":[11],"domains":[12],"(VHHs),":[13],"which":[14,81],"retain":[15],"antigen-binding":[16],"functionality":[17],"even":[18],"when":[19],"isolated.":[20],"The":[21,123],"term":[22],"\"nanobody\"":[23],"is":[24],"now":[25],"more":[26],"generally":[27],"used":[28],"for":[29,41,67,92],"describing":[30],"small,":[31],"single-domain":[32],"antibodies.":[33],"Several":[34],"antibody":[35],"generative":[36,99],"models":[37,63],"have":[38],"been":[39],"developed":[40],"the":[42,48,54,138,157],"sequence":[43],"structure":[45],"co-design":[46],"complementarity-determining":[49],"regions":[50],"(CDRs)":[51],"based":[52,97,116],"on":[53,76,98,117,146],"binding":[55],"interface":[56],"with":[57],"a":[58,90,134],"target":[59],"antigen.":[60],"However,":[61],"these":[62],"are":[64,70,82],"not":[65],"tailored":[66],"nanobodies":[68],"often":[71],"constrained":[72],"by":[73],"their":[74],"reliance":[75],"experimentally":[77],"determined":[78],"antigen-antibody":[79],"structures,":[80],"labor-intensive":[83],"to":[84,150],"obtain.":[85],"Here,":[86],"we":[87],"introduce":[88],"NanoDesigner,":[89],"tool":[91],"nanobody":[93,163],"design":[94],"optimization":[96],"AI":[100],"methods.":[101],"NanoDesigner":[102,154],"integrates":[103],"key":[104],"stages-structure":[105],"prediction,":[106],"docking,":[107],"CDR":[108,139,143,171],"generation,":[109],"side-chain":[111],"packing-into":[112],"an":[113,118,127],"iterative":[114],"framework":[115],"expectation":[119],"maximization":[120],"(EM)":[121],"algorithm.":[122],"algorithm":[124],"effectively":[125],"tackles":[126],"interdependency":[128],"challenge":[129],"where":[130],"accurate":[131,147],"docking":[132,148,169],"presupposes":[133],"priori":[135],"knowledge":[136],"conformation,":[140],"while":[141],"effective":[142],"generation":[144],"relies":[145],"outputs":[149],"guide":[151],"its":[152],"design.":[153],"approximately":[155],"doubles":[156],"success":[158],"rate":[159],"de":[161],"novo":[162],"designs":[164],"through":[165],"continuous":[166],"refinement":[167],"generation.":[172]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
