{"id":"https://openalex.org/W4391539510","doi":"https://doi.org/10.1007/s11227-023-05887-9","title":"Antibody complementarity-determining region design using AlphaFold2 and DDG predictor","display_name":"Antibody complementarity-determining region design using AlphaFold2 and DDG predictor","publication_year":2024,"publication_date":"2024-02-05","ids":{"openalex":"https://openalex.org/W4391539510","doi":"https://doi.org/10.1007/s11227-023-05887-9"},"language":"en","primary_location":{"id":"doi:10.1007/s11227-023-05887-9","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11227-023-05887-9","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05887-9.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"The Journal of Supercomputing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05887-9.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113173616","display_name":"Takafumi Ueki","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takafumi Ueki","raw_affiliation_strings":["Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, Yokohama City, 226-8501, Kanagawa, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, Yokohama City, 226-8501, Kanagawa, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061510293","display_name":"Masahito Ohue","orcid":"https://orcid.org/0000-0002-0120-1643"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Masahito Ohue","raw_affiliation_strings":["Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, Yokohama City, 226-8501, Kanagawa, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, Yokohama City, 226-8501, Kanagawa, Japan","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5061510293"],"corresponding_institution_ids":["https://openalex.org/I114531698"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":2.1403,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.86682225,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"80","issue":"9","first_page":"11989","last_page":"12002"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"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/T11124","display_name":"Protein purification and stability","score":0.9941999912261963,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9934999942779541,"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/complementarity","display_name":"Complementarity (molecular biology)","score":0.7542423009872437},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.7097116112709045},{"id":"https://openalex.org/keywords/complementarity-determining-region","display_name":"Complementarity determining region","score":0.6977078914642334},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5634598135948181},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.555534839630127},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein engineering","score":0.5397459268569946},{"id":"https://openalex.org/keywords/affinity-maturation","display_name":"Affinity maturation","score":0.5330373644828796},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4628450572490692},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4597499668598175},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.43887725472450256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3128567337989807},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.30710408091545105},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1737200915813446},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.16485321521759033},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12445217370986938},{"id":"https://openalex.org/keywords/monoclonal-antibody","display_name":"Monoclonal antibody","score":0.11593079566955566},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.10571998357772827}],"concepts":[{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.7542423009872437},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.7097116112709045},{"id":"https://openalex.org/C85630698","wikidata":"https://www.wikidata.org/wiki/Q3826179","display_name":"Complementarity determining region","level":4,"score":0.6977078914642334},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5634598135948181},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.555534839630127},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.5397459268569946},{"id":"https://openalex.org/C2781377902","wikidata":"https://www.wikidata.org/wiki/Q21418769","display_name":"Affinity maturation","level":3,"score":0.5330373644828796},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4628450572490692},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4597499668598175},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.43887725472450256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3128567337989807},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.30710408091545105},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1737200915813446},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.16485321521759033},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12445217370986938},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.11593079566955566},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.10571998357772827},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s11227-023-05887-9","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11227-023-05887-9","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05887-9.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"The Journal of Supercomputing","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s11227-023-05887-9","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11227-023-05887-9","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05887-9.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"The Journal of Supercomputing","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3897611434","display_name":null,"funder_award_id":"KAKENHI 23H03496","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5608217151","display_name":"Development of cyclic peptide-protein complex structure database and peptide design method","funder_award_id":"23K28186","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G733518665","display_name":null,"funder_award_id":"FOREST JPMJFR216J","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391539510.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1982679430","https://openalex.org/W2010537388","https://openalex.org/W2070505228","https://openalex.org/W2140673705","https://openalex.org/W2283896596","https://openalex.org/W2805822355","https://openalex.org/W2980789587","https://openalex.org/W2993866869","https://openalex.org/W3037592148","https://openalex.org/W3154275519","https://openalex.org/W3177828909","https://openalex.org/W3183475563","https://openalex.org/W3186179742","https://openalex.org/W3216341763","https://openalex.org/W4214886481","https://openalex.org/W4284710673","https://openalex.org/W4289522536","https://openalex.org/W4308918781","https://openalex.org/W4310159409","https://openalex.org/W4386222188","https://openalex.org/W4394629166"],"related_works":["https://openalex.org/W2016103121","https://openalex.org/W2892228640","https://openalex.org/W2093380070","https://openalex.org/W3095061474","https://openalex.org/W1972242350","https://openalex.org/W3143922975","https://openalex.org/W4387734409","https://openalex.org/W2106522450","https://openalex.org/W2087117158","https://openalex.org/W2108020478"],"abstract_inverted_index":{"Abstract":[0],"The":[1,64],"constraints":[2],"imposed":[3],"by":[4],"natural":[5],"antibody":[6,27,43,104,169],"affinity":[7,29,110],"maturation":[8],"often":[9],"culminate":[10],"in":[11,59,129,155],"antibodies":[12,147],"with":[13,94,125,148],"suboptimal":[14],"binding":[15,28,109],"affinities,":[16],"thereby":[17],"limiting":[18],"their":[19],"therapeutic":[20],"efficacy.":[21],"As":[22],"such,":[23],"the":[24,33,52,60,77,89,95,100,108,118,130,140],"augmentation":[25],"of":[26,35,56,66,82,91,103,111,132],"is":[30,143],"pivotal":[31],"for":[32,42,76,99,151,168],"advancement":[34],"efficacious":[36],"antibody-based":[37],"therapies.":[38],"Classical":[39],"experimental":[40],"paradigms":[41],"engineering":[44],"are":[45],"financially":[46],"and":[47,73,80,165],"temporally":[48],"prohibitive":[49],"due":[50],"to":[51,106,120],"extensive":[53],"combinatorial":[54],"space":[55],"sequence":[57],"variations":[58],"complementarity-determining":[61],"regions":[62],"(CDRs).":[63],"advent":[65],"computational":[67,101],"techniques":[68],"presents":[69],"a":[70,163],"more":[71],"expeditious":[72],"economical":[74],"avenue":[75],"systematic":[78],"design":[79],"optimization":[81],"antibodies.":[83],"In":[84],"this":[85],"investigation,":[86],"we":[87],"assess":[88],"performance":[90],"AlphaFold2":[92],"coupled":[93],"binder":[96],"hallucination":[97],"technique":[98],"refinement":[102],"sequences":[105],"elevate":[107],"pre-existing":[112],"antigen-antibody":[113,152],"complexes.":[114],"These":[115],"methodologies":[116],"exhibit":[117],"capability":[119],"predict":[121],"protein":[122],"tertiary":[123],"structures":[124],"remarkable":[126],"fidelity,":[127],"even":[128],"absence":[131],"empirically":[133],"derived":[134],"data.":[135],"Our":[136],"results":[137],"intimate":[138],"that":[139],"proposed":[141],"approach":[142],"adept":[144],"at":[145],"designing":[146],"improved":[149],"affinities":[150],"complexes":[153],"unrepresented":[154],"AlphaFold2\u2019s":[156],"training":[157],"dataset,":[158],"underscoring":[159],"its":[160],"potential":[161],"as":[162],"robust":[164],"scalable":[166],"strategy":[167],"engineering.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}