{"id":"https://openalex.org/W2022670869","doi":"https://doi.org/10.1145/1854776.1854894","title":"An automatic computational pipeline to display MHC binding motifs","display_name":"An automatic computational pipeline to display MHC binding motifs","publication_year":2010,"publication_date":"2010-08-02","ids":{"openalex":"https://openalex.org/W2022670869","doi":"https://doi.org/10.1145/1854776.1854894","mag":"2022670869"},"language":"en","primary_location":{"id":"doi:10.1145/1854776.1854894","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854894","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","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/A5100396031","display_name":"Peng Wang","orcid":"https://orcid.org/0000-0002-4534-2691"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Wang","raw_affiliation_strings":["La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023547268","display_name":"Bjoern Peters","orcid":"https://orcid.org/0000-0002-8457-6693"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bjoern Peters","raw_affiliation_strings":["La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037285448","display_name":"John Sidney","orcid":"https://orcid.org/0000-0002-0987-405X"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Sidney","raw_affiliation_strings":["La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110063666","display_name":"Alex Sette","orcid":null},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Sette","raw_affiliation_strings":["La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"La Jolla Institute for Allergy &amp; Immunology, La Jolla, CA","institution_ids":["https://openalex.org/I1311191458"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1311191458"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12591508,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"634","last_page":"641"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"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":1.0,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9941999912261963,"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"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9934999942779541,"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/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.7730355262756348},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5943121314048767},{"id":"https://openalex.org/keywords/mhc-class-i","display_name":"MHC class I","score":0.5473211407661438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5316855311393738},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5197046399116516},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.4315694570541382},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3773690164089203},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25915825366973877},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.23805579543113708},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09112176299095154}],"concepts":[{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.7730355262756348},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5943121314048767},{"id":"https://openalex.org/C170627219","wikidata":"https://www.wikidata.org/wiki/Q13218497","display_name":"MHC class I","level":4,"score":0.5473211407661438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5316855311393738},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5197046399116516},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.4315694570541382},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3773690164089203},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25915825366973877},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.23805579543113708},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09112176299095154}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1854776.1854894","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854894","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G116422006","display_name":null,"funder_award_id":"HHSN26620040006C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1549641435","https://openalex.org/W1786753252","https://openalex.org/W1971302107","https://openalex.org/W1981106544","https://openalex.org/W1982271112","https://openalex.org/W1991461541","https://openalex.org/W1994048581","https://openalex.org/W2009703634","https://openalex.org/W2028339001","https://openalex.org/W2041877620","https://openalex.org/W2100412095","https://openalex.org/W2103498243","https://openalex.org/W2110574412","https://openalex.org/W2120399005","https://openalex.org/W2125014261","https://openalex.org/W2125732073","https://openalex.org/W2158266834","https://openalex.org/W2159404298"],"related_works":["https://openalex.org/W2205639271","https://openalex.org/W1840653008","https://openalex.org/W2977793531","https://openalex.org/W2023967363","https://openalex.org/W1939527068","https://openalex.org/W2126139339","https://openalex.org/W2168688111","https://openalex.org/W2070684866","https://openalex.org/W4281625971","https://openalex.org/W2094567316"],"abstract_inverted_index":{"The":[0,23,135],"major":[1],"histocompatibility":[2],"complex":[3],"(MHC)":[4],"class":[5,121],"I":[6,122],"molecules":[7,27,69,123],"play":[8],"key":[9,61],"roles":[10],"in":[11,70],"host":[12],"immunity":[13],"against":[14],"pathogens":[15],"by":[16],"presenting":[17],"peptide":[18,49,84],"antigens":[19],"to":[20,31,47,59],"CD8+":[21],"T-cells.":[22],"hallmark":[24],"of":[25,96,118],"MHC":[26,50,68,85,120,156],"is":[28],"their":[29],"capacity":[30],"present":[32,78],"peptides":[33],"with":[34,131],"tremendous":[35],"sequence":[36],"diversity.":[37],"Both":[38],"experimental":[39],"approaches":[40],"and":[41,90,124,145,149],"computational":[42,80],"algorithms":[43,114],"have":[44],"been":[45,138],"utilized":[46],"analyze":[48],"binding":[51,62,86,97,108],"characteristics.":[52],"However,":[53],"it":[54],"remains":[55],"a":[56,67,79,92,102,116],"challenging":[57],"task":[58],"summarize":[60],"properties":[63],"for":[64],"large":[65],"number":[66],"an":[71],"automatic":[72,113],"fashion.":[73],"In":[74],"this":[75],"paper,":[76],"we":[77],"pipeline":[81,136],"that":[82,105,126],"takes":[83],"data":[87],"as":[88,99,101],"input":[89],"produces":[91],"cartoon":[93],"like":[94],"summary":[95],"motif":[98],"well":[100],"colored":[103],"matrix":[104],"displays":[106],"detailed":[107],"information.":[109],"We":[110],"tested":[111],"our":[112,127],"on":[115],"set":[117],"18":[119],"showed":[125],"predictions":[128],"are":[129],"consistent":[130],"historic":[132],"manual":[133],"assignments.":[134],"has":[137],"incorporated":[139],"into":[140],"the":[141],"immune":[142],"epitope":[143],"database":[144],"analysis":[146],"resource":[147],"(IEDB)":[148],"motifs":[150],"can":[151],"be":[152],"visualized":[153],"while":[154],"browsing":[155],"alleles":[157],"through":[158],"IEDB.":[159]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
