{"id":"https://openalex.org/W3164228670","doi":"https://doi.org/10.1109/tcbb.2021.3083001","title":"Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction","display_name":"Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction","publication_year":2021,"publication_date":"2021-05-24","ids":{"openalex":"https://openalex.org/W3164228670","doi":"https://doi.org/10.1109/tcbb.2021.3083001","mag":"3164228670","pmid":"https://pubmed.ncbi.nlm.nih.gov/34029193"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3083001","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3083001","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015725187","display_name":"Shuai Lu","orcid":"https://orcid.org/0000-0001-9489-0611"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shuai Lu","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, China","institution_ids":["https://openalex.org/I38877650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039487617","display_name":"Yuguang Li","orcid":"https://orcid.org/0000-0002-8927-3536"},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuguang Li","raw_affiliation_strings":["College of Economics and Management, Zhengzhou University of Light Industry, Zhengzhou, Henan, China"],"affiliations":[{"raw_affiliation_string":"College of Economics and Management, Zhengzhou University of Light Industry, Zhengzhou, Henan, China","institution_ids":["https://openalex.org/I23171815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100455844","display_name":"Fei Wang","orcid":"https://orcid.org/0000-0002-5666-5293"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Wang","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, China","institution_ids":["https://openalex.org/I38877650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038837906","display_name":"Xiaofei Nan","orcid":"https://orcid.org/0000-0001-9145-1111"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofei Nan","raw_affiliation_strings":["School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhengzhou University, Zhengzhou, Henan, China","institution_ids":["https://openalex.org/I38877650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101478100","display_name":"Shoutao Zhang","orcid":"https://orcid.org/0000-0002-0152-395X"},"institutions":[{"id":"https://openalex.org/I38877650","display_name":"Zhengzhou University","ror":"https://ror.org/04ypx8c21","country_code":"CN","type":"education","lineage":["https://openalex.org/I38877650"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shoutao Zhang","raw_affiliation_strings":["School of Life Science, Zhengzhou University, Zhengzhou, Henan, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Zhengzhou University, Zhengzhou, Henan, China","institution_ids":["https://openalex.org/I38877650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5015725187"],"corresponding_institution_ids":["https://openalex.org/I38877650"],"apc_list":null,"apc_paid":null,"fwci":1.512,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.82087865,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"68","last_page":"74"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"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":1.0,"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":0.9991000294685364,"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":0.9983999729156494,"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/paratope","display_name":"Paratope","score":0.6935412287712097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6273955702781677},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5009875297546387},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4912514090538025},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.46508070826530457},{"id":"https://openalex.org/keywords/convolution","display_name":"Convolution (computer science)","score":0.4480656385421753},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.443763792514801},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4221068024635315},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3729652166366577},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25328177213668823},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21882975101470947},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.2076520025730133},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.18786606192588806}],"concepts":[{"id":"https://openalex.org/C9086966","wikidata":"https://www.wikidata.org/wiki/Q489135","display_name":"Paratope","level":4,"score":0.6935412287712097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6273955702781677},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5009875297546387},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4912514090538025},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.46508070826530457},{"id":"https://openalex.org/C45347329","wikidata":"https://www.wikidata.org/wiki/Q5166604","display_name":"Convolution (computer science)","level":3,"score":0.4480656385421753},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.443763792514801},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4221068024635315},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3729652166366577},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25328177213668823},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21882975101470947},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2076520025730133},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.18786606192588806}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001666","descriptor_name":"Binding Sites, Antibody","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3083001","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3083001","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34029193","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34029193","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1500927176","https://openalex.org/W1829437510","https://openalex.org/W1997875463","https://openalex.org/W2007054796","https://openalex.org/W2008708467","https://openalex.org/W2073229442","https://openalex.org/W2103148772","https://openalex.org/W2117012297","https://openalex.org/W2127771490","https://openalex.org/W2128673241","https://openalex.org/W2132580736","https://openalex.org/W2138104170","https://openalex.org/W2139516171","https://openalex.org/W2147209844","https://openalex.org/W2150014697","https://openalex.org/W2150884352","https://openalex.org/W2158714788","https://openalex.org/W2165242943","https://openalex.org/W2167833742","https://openalex.org/W2751808960","https://openalex.org/W2757376023","https://openalex.org/W2790912632","https://openalex.org/W2801127413","https://openalex.org/W2801965704","https://openalex.org/W2808491442","https://openalex.org/W2900437486","https://openalex.org/W2901312940","https://openalex.org/W2970971581","https://openalex.org/W3010441732","https://openalex.org/W3014745572","https://openalex.org/W3016492430","https://openalex.org/W3042835606","https://openalex.org/W3122210777","https://openalex.org/W4236258478","https://openalex.org/W4293003482","https://openalex.org/W4295312788","https://openalex.org/W6743410771","https://openalex.org/W6780560506"],"related_works":["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/W3138783506","https://openalex.org/W2498359070","https://openalex.org/W3167731532","https://openalex.org/W2066154019"],"abstract_inverted_index":{"Antibodies":[0],"consisting":[1],"of":[2,11,20,33,43,50,68,101,116,127],"variable":[3],"and":[4,39,53,83,106],"constant":[5],"regions,":[6],"are":[7],"a":[8,14,30,60],"special":[9],"type":[10],"proteins":[12],"playing":[13],"vital":[15],"role":[16],"in":[17],"immune":[18],"system":[19],"the":[21,25,79,113,124,139],"vertebrate.":[22],"They":[23],"have":[24],"remarkable":[26],"ability":[27],"to":[28,62,98,109],"bind":[29],"large":[31],"range":[32],"diverse":[34],"antigens":[35],"with":[36,73,93],"extraordinary":[37],"affinity":[38],"specificity.":[40],"This":[41],"malleability":[42],"binding":[44],"makes":[45],"antibodies":[46],"an":[47,69,128,132],"important":[48],"class":[49],"biological":[51],"drugs":[52],"biomarkers.":[54],"In":[55],"this":[56],"article,":[57],"we":[58,122],"propose":[59],"method":[61,136],"identify":[63],"which":[64],"amino":[65,118],"acid":[66,119],"residues":[67],"antibody":[70,129],"directly":[71],"interact":[72],"its":[74],"associated":[75],"antigen":[76,125],"based":[77],"on":[78,138],"features":[80],"from":[81,103],"sequence":[82],"structure.":[84],"Our":[85,135],"algorithm":[86],"uses":[87],"convolution":[88,95],"neural":[89],"networks":[90,96],"(CNNs)":[91],"linked":[92],"graph":[94],"(GCNs)":[97],"make":[99],"use":[100],"information":[102],"both":[104],"sequential":[105],"spatial":[107],"neighbors":[108],"understand":[110],"more":[111],"about":[112],"local":[114],"environment":[115],"target":[117],"residue.":[120],"Furthermore,":[121],"process":[123],"partner":[126],"by":[130],"employing":[131],"attention":[133],"layer.":[134],"improves":[137],"state-of-the-art":[140],"methodology.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
