{"id":"https://openalex.org/W4394731490","doi":"https://doi.org/10.1145/3647817.3647820","title":"PepTracR: a Centralized Database for Pathogen Peptides and Neoepitopes based on 3D Structures information and Similarity-search in T-cell Immunotherapy Research","display_name":"PepTracR: a Centralized Database for Pathogen Peptides and Neoepitopes based on 3D Structures information and Similarity-search in T-cell Immunotherapy Research","publication_year":2023,"publication_date":"2023-10-20","ids":{"openalex":"https://openalex.org/W4394731490","doi":"https://doi.org/10.1145/3647817.3647820"},"language":"en","primary_location":{"id":"doi:10.1145/3647817.3647820","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3647817.3647820","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 12th International Conference on Bioinformatics and Biomedical Science","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5021450810","display_name":"Tao-Chuan Shih","orcid":"https://orcid.org/0000-0003-0583-0858"},"institutions":[{"id":"https://openalex.org/I118292597","display_name":"National Taipei University of Technology","ror":"https://ror.org/00cn92c09","country_code":"TW","type":"education","lineage":["https://openalex.org/I118292597"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Tao-Chuan Shih","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Taipei University of Technology, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-0583-0858","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Taipei University of Technology, Taiwan","institution_ids":["https://openalex.org/I118292597"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077115938","display_name":"Cing-Han Yang","orcid":"https://orcid.org/0009-0000-8026-1822"},"institutions":[{"id":"https://openalex.org/I153512688","display_name":"National Taiwan Ocean University","ror":"https://ror.org/03bvvnt49","country_code":"TW","type":"education","lineage":["https://openalex.org/I153512688"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Cing-Han Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, National Taiwan Ocean University, Taiwan"],"raw_orcid":"https://orcid.org/0009-0000-8026-1822","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, National Taiwan Ocean University, Taiwan","institution_ids":["https://openalex.org/I153512688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006860006","display_name":"Ying-Ja Chen","orcid":"https://orcid.org/0009-0004-0218-8219"},"institutions":[{"id":"https://openalex.org/I4210143126","display_name":"Acer (Taiwan)","ror":"https://ror.org/03xajsx66","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210143126"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Ying-Ja Chen","raw_affiliation_strings":["ACER, Taiwan"],"raw_orcid":"https://orcid.org/0009-0004-0218-8219","affiliations":[{"raw_affiliation_string":"ACER, Taiwan","institution_ids":["https://openalex.org/I4210143126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059307693","display_name":"Li\u2010Tzu Yeh","orcid":"https://orcid.org/0000-0003-2351-8040"},"institutions":[{"id":"https://openalex.org/I4210143126","display_name":"Acer (Taiwan)","ror":"https://ror.org/03xajsx66","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210143126"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Li-Tzu Yeh","raw_affiliation_strings":["ACER, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-2351-8040","affiliations":[{"raw_affiliation_string":"ACER, Taiwan","institution_ids":["https://openalex.org/I4210143126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002359792","display_name":"Chi-Wei Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143126","display_name":"Acer (Taiwan)","ror":"https://ror.org/03xajsx66","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210143126"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chi-Wei Lu","raw_affiliation_strings":["ACER, Taiwan"],"raw_orcid":"https://orcid.org/0009-0006-7920-8905","affiliations":[{"raw_affiliation_string":"ACER, Taiwan","institution_ids":["https://openalex.org/I4210143126"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086428506","display_name":"Tun\u2010Wen Pai","orcid":"https://orcid.org/0000-0002-2869-4169"},"institutions":[{"id":"https://openalex.org/I118292597","display_name":"National Taipei University of Technology","ror":"https://ror.org/00cn92c09","country_code":"TW","type":"education","lineage":["https://openalex.org/I118292597"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tun-Wen Pai","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Taipei University of Technology, Taiwan"],"raw_orcid":"https://orcid.org/0000-0002-2869-4169","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Taipei University of Technology, Taiwan","institution_ids":["https://openalex.org/I118292597"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5021450810"],"corresponding_institution_ids":["https://openalex.org/I118292597"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.35574344,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"17","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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":0.9796000123023987,"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/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.968500018119812,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6268720030784607},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6020670533180237},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.5741643905639648},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.5045913457870483},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4993417263031006},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.42725950479507446},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3987601101398468},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.2614189684391022},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.25304070115089417},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23842188715934753},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20766955614089966},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.19888374209403992}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6268720030784607},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6020670533180237},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.5741643905639648},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.5045913457870483},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4993417263031006},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.42725950479507446},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3987601101398468},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.2614189684391022},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25304070115089417},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23842188715934753},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20766955614089966},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.19888374209403992},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3647817.3647820","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3647817.3647820","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 12th International Conference on Bioinformatics and Biomedical Science","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2051152071","https://openalex.org/W2156654829","https://openalex.org/W2613978126","https://openalex.org/W2752126733","https://openalex.org/W2953065444","https://openalex.org/W2955439997","https://openalex.org/W2965921152","https://openalex.org/W2995494055","https://openalex.org/W3008682585","https://openalex.org/W3154423121","https://openalex.org/W4302424609"],"related_works":["https://openalex.org/W4292296636","https://openalex.org/W1963790256","https://openalex.org/W2090768198","https://openalex.org/W4206415530","https://openalex.org/W2074014730","https://openalex.org/W2383633458","https://openalex.org/W3194411068","https://openalex.org/W2105075449","https://openalex.org/W22579956","https://openalex.org/W2114617504"],"abstract_inverted_index":{"T-cell":[0,26,34,73,89,168],"receptors":[1],"(TCRs)":[2],"are":[3,50],"essential":[4],"proteins":[5],"on":[6],"T":[7],"cells":[8],"recognizing":[9],"antigens":[10],"presented":[11],"by":[12,107],"MHC":[13],"molecules.":[14],"They\u2019re":[15],"pivotal":[16],"in":[17],"immune":[18],"responses":[19,37],"to":[20,38,53,97,157,179],"infections":[21],"(pathogens)":[22],"and":[23,30,36,43,48,56,69,87,117,144,166,173,181],"cancers":[24],"(neoepitopes).":[25],"assays":[27],"like":[28],"ELISpot":[29],"cytokine":[31],"production":[32],"gauge":[33],"recognition":[35],"these":[39],"antigens.":[40],"However,":[41],"gathering":[42],"representing":[44],"data":[45,57,71,86,122,165],"from":[46],"IEDB":[47],"others":[49],"complex":[51],"due":[52],"naming":[54,114],"conventions":[55],"issues.To":[58],"overcome":[59],"this,":[60],"a":[61,81],"centralized":[62],"database":[63],"is":[64,77,156],"crucial,":[65],"uniting":[66],"pathogen":[67,93,103],"peptide":[68,141],"neoepitope":[70,85,160,182],"with":[72,95,127],"assay":[74,169],"info.":[75,153],"PepTracR":[76,132,176],"our":[78],"solution":[79],"-":[80],"comprehensive":[82],"resource":[83],"for":[84,139],"corresponding":[88],"assays.":[90],"It":[91],"aids":[92],"studies":[94],"functions":[96],"search":[98],"against":[99],"human":[100],"genome":[101],"or":[102,129],"protein":[104],"sequences,":[105],"supported":[106],"sequence":[108,134],"alignment.":[109],"Our":[110,154],"script":[111],"updates":[112,150],"old":[113],"conventions.":[115],"StcrDab":[116],"TCR3D":[118],"integration":[119],"provides":[120],"structural":[121],"through":[123],"alignment,":[124],"displaying":[125],"interactions":[126],"JSmol":[128],"graphical":[130],"diagrams.":[131],"applies":[133],"motifs,":[135],"peptide-MHC":[136,145],"prediction":[137],"tools":[138],"CDR-pathogen":[140],"diversity":[142],"analysis,":[143],"binding":[146],"affinity":[147],"evaluation.":[148],"Regular":[149],"ensure":[151],"current":[152],"aim":[155],"serve":[158],"the":[159],"research":[161,183],"community,":[162],"organizing":[163],"curated":[164],"granting":[167],"access.":[170],"Utilizing":[171],"self-similarity":[172],"pathogen-similarity":[174],"tools,":[175],"contributes":[177],"effectively":[178],"pathogen-peptide":[180]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}