{"id":"https://openalex.org/W4225492932","doi":"https://doi.org/10.1109/bibm52615.2021.9669631","title":"DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks","display_name":"DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4225492932","doi":"https://doi.org/10.1109/bibm52615.2021.9669631"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669631","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669631","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://research-repository.griffith.edu.au/bitstreams/13d8ace7-3682-4b84-bcd2-f2baf62b69c0/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100406352","display_name":"Pan Zhang","orcid":"https://orcid.org/0000-0002-9462-9840"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Pan Zhang","raw_affiliation_strings":["School of Computer Science, Sun Yat-sen University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075817762","display_name":"Shuangjia Zheng","orcid":"https://orcid.org/0000-0001-9747-4285"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuangjia Zheng","raw_affiliation_strings":["School of Computer Science, Galixir & Sun Yat-sen University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Galixir & Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100689463","display_name":"Jianwen Chen","orcid":"https://orcid.org/0000-0001-7999-2070"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianwen Chen","raw_affiliation_strings":["School of Computer Science, Sun Yat-sen University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032724151","display_name":"Yaoqi Zhou","orcid":"https://orcid.org/0000-0002-9958-5699"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaoqi Zhou","raw_affiliation_strings":["Institute for Systems and Physical Biology Shenzhen Bay Laboratory & Peking, University Shenzhen Graduate School, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Institute for Systems and Physical Biology Shenzhen Bay Laboratory & Peking, University Shenzhen Graduate School, Shenzhen, China","institution_ids":["https://openalex.org/I4210102541","https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["School of Computer Science, Sun Yat-sen University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100406352"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":null,"apc_paid":null,"fwci":0.6067,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.62792453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"577","issue":null,"first_page":"118","last_page":"124"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9994000196456909,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/paratope","display_name":"Paratope","score":0.9573861360549927},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7441537380218506},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3769133687019348},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.351718008518219},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.23651468753814697},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1963512897491455},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1275312602519989}],"concepts":[{"id":"https://openalex.org/C9086966","wikidata":"https://www.wikidata.org/wiki/Q489135","display_name":"Paratope","level":4,"score":0.9573861360549927},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7441537380218506},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3769133687019348},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.351718008518219},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.23651468753814697},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1963512897491455},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1275312602519989}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669631","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669631","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/413882","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/413882","pdf_url":"https://research-repository.griffith.edu.au/bitstreams/13d8ace7-3682-4b84-bcd2-f2baf62b69c0/download","source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference output"}],"best_oa_location":{"id":"pmh:oai:research-repository.griffith.edu.au:10072/413882","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/413882","pdf_url":"https://research-repository.griffith.edu.au/bitstreams/13d8ace7-3682-4b84-bcd2-f2baf62b69c0/download","source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference output"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1477544716","display_name":null,"funder_award_id":"Guangdong","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2602136225","display_name":null,"funder_award_id":"2018B01","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2981938667","display_name":null,"funder_award_id":"Shenzhen","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3085993365","display_name":null,"funder_award_id":"(Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3866723802","display_name":null,"funder_award_id":"201703","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5108781970","display_name":null,"funder_award_id":"61772566","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5178878423","display_name":null,"funder_award_id":"2020YFB0204803","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6069953956","display_name":null,"funder_award_id":"2018B0101","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6346021793","display_name":null,"funder_award_id":"2019B020228001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8208342437","display_name":null,"funder_award_id":"1 and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8412750340","display_name":null,"funder_award_id":"2017033","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8955107213","display_name":null,"funder_award_id":"Major","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G962820005","display_name":null,"funder_award_id":"S201101001","funder_id":"https://openalex.org/F4320331248","funder_display_name":"Shenzhen Bay Laboratory"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320331248","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4225492932.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1508583216","https://openalex.org/W1522301498","https://openalex.org/W1829437510","https://openalex.org/W1896254721","https://openalex.org/W1963778872","https://openalex.org/W2045080704","https://openalex.org/W2064675550","https://openalex.org/W2092067482","https://openalex.org/W2094052190","https://openalex.org/W2110505462","https://openalex.org/W2117012297","https://openalex.org/W2131774270","https://openalex.org/W2132083787","https://openalex.org/W2132580736","https://openalex.org/W2141014056","https://openalex.org/W2143467722","https://openalex.org/W2152575748","https://openalex.org/W2158714788","https://openalex.org/W2515530302","https://openalex.org/W2557595285","https://openalex.org/W2607268717","https://openalex.org/W2766736793","https://openalex.org/W2801965704","https://openalex.org/W2808491442","https://openalex.org/W2915163461","https://openalex.org/W2953384591","https://openalex.org/W2999044305","https://openalex.org/W3005769002","https://openalex.org/W3122210777","https://openalex.org/W4385245566","https://openalex.org/W6631190155","https://openalex.org/W6713134421","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2093006382","https://openalex.org/W3094563030","https://openalex.org/W4285597652","https://openalex.org/W2917097596","https://openalex.org/W3130759820","https://openalex.org/W4229020575","https://openalex.org/W3167731532","https://openalex.org/W2029994374"],"abstract_inverted_index":{"Antibodies":[0],"are":[1],"a":[2,72,141],"type":[3],"of":[4,27,54,66,115],"important":[5],"biomolecules":[6],"in":[7],"the":[8,28,30,64,100,103,106,113,116],"humoral":[9],"immunity":[10],"system,":[11],"which":[12],"can":[13],"bind":[14],"tightly":[15],"to":[16,75,98,111],"potential":[17],"antigens":[18],"with":[19,33],"high":[20],"affinity":[21],"and":[22,41,83,95,110,145],"specificity.":[23],"An":[24],"accurate":[25],"identification":[26],"paratope,":[29],"binding":[31],"sites":[32],"antigens,":[34],"is":[35,57,137],"crucial":[36],"for":[37,49,87,146],"antibody":[38,74,129],"mechanistic":[39],"research":[40],"design.":[42],"Although":[43],"many":[44],"methods":[45,132],"have":[46],"been":[47],"developed":[48],"paratope":[50,89,130],"prediction,":[51],"further":[52,92],"improvement":[53],"their":[55],"accuracy":[56],"necessary.":[58],"In":[59],"this":[60],"study,":[61],"we":[62],"concatenated":[63,107],"sequences":[65,109],"Complementarity":[67],"Determining":[68],"Regions":[69],"(CDRs)":[70],"within":[71,105],"single":[73],"better":[76],"capture":[77],"nonlocal":[78],"interactions":[79],"between":[80],"different":[81],"CDRs":[82],"loop":[84],"type-specific":[85],"features":[86],"improving":[88],"prediction.":[90],"We":[91],"integrated":[93],"BiLSTM":[94],"transformer":[96],"networks":[97],"gain":[99],"dependencies":[101],"among":[102],"residues":[104],"CDR":[108],"increase":[112],"interpretability":[114],"model.":[117],"The":[118,134],"new":[119],"method":[120,136],"called":[121],"DeepANIS":[122,135],"(Antibody":[123],"Interacting":[124],"Site":[125],"prediction)":[126],"outperforms":[127],"other":[128],"prediction":[131],"compared.":[133],"freely":[138],"available":[139],"as":[140],"webserver":[142],"at":[143,148],"https://biomed.nscc-gz.cn/apps/DeepANIS":[144],"download":[147],"https://github.com/HideInDust/DeepANIS.":[149]},"counts_by_year":[{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
