{"id":"https://openalex.org/W3004851229","doi":"https://doi.org/10.1109/bibm47256.2019.8983260","title":"Prediction of proteasomal cleavage sites using PCPS","display_name":"Prediction of proteasomal cleavage sites using PCPS","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004851229","doi":"https://doi.org/10.1109/bibm47256.2019.8983260","mag":"3004851229"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983260","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983260","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5005649006","display_name":"Marta Gomez\u2010Perosanz","orcid":"https://orcid.org/0000-0002-2411-4358"},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marta Gomez-Perosanz","raw_affiliation_strings":["Complutense University of Madrid,Faculty of Medicine,Department of Immunology,Madrid,Spain","Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complutense University of Madrid,Faculty of Medicine,Department of Immunology,Madrid,Spain","institution_ids":["https://openalex.org/I121748325"]},{"raw_affiliation_string":"Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076050008","display_name":"Alvaro Ras-Carmona","orcid":"https://orcid.org/0000-0003-1644-6878"},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alvaro Ras-Carmona","raw_affiliation_strings":["Complutense University of Madrid,Faculty of Medicine,Department of Immunology,Madrid,Spain","Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complutense University of Madrid,Faculty of Medicine,Department of Immunology,Madrid,Spain","institution_ids":["https://openalex.org/I121748325"]},{"raw_affiliation_string":"Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain","institution_ids":["https://openalex.org/I121748325"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051034667","display_name":"Pedro A. Reche","orcid":"https://orcid.org/0000-0003-3966-5838"},"institutions":[{"id":"https://openalex.org/I121748325","display_name":"Universidad Complutense de Madrid","ror":"https://ror.org/02p0gd045","country_code":"ES","type":"education","lineage":["https://openalex.org/I121748325"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pedro A. Reche","raw_affiliation_strings":["Complutense University of Madrid,Faculty of Medicine,Department of Immunology,Madrid,Spain","Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complutense University of Madrid,Faculty of Medicine,Department of Immunology,Madrid,Spain","institution_ids":["https://openalex.org/I121748325"]},{"raw_affiliation_string":"Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain","institution_ids":["https://openalex.org/I121748325"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I121748325"],"apc_list":null,"apc_paid":null,"fwci":0.171,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54412703,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"2137","last_page":"2140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11041","display_name":"Ubiquitin and proteasome pathways","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/T11041","display_name":"Ubiquitin and proteasome pathways","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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9965000152587891,"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/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.9921000003814697,"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/cleavage","display_name":"Cleavage (geology)","score":0.6822850108146667},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42215773463249207},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.34387195110321045},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.24002805352210999},{"id":"https://openalex.org/keywords/composite-material","display_name":"Composite material","score":0.07267948985099792}],"concepts":[{"id":"https://openalex.org/C175156509","wikidata":"https://www.wikidata.org/wiki/Q1990218","display_name":"Cleavage (geology)","level":3,"score":0.6822850108146667},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42215773463249207},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34387195110321045},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.24002805352210999},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.07267948985099792},{"id":"https://openalex.org/C43369102","wikidata":"https://www.wikidata.org/wiki/Q2307625","display_name":"Fracture (geology)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983260","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983260","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5299999713897705,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1543322656","https://openalex.org/W1559325378","https://openalex.org/W1967731044","https://openalex.org/W1977142804","https://openalex.org/W2073621589","https://openalex.org/W2087137589","https://openalex.org/W2091493030","https://openalex.org/W2102054691","https://openalex.org/W2102237050","https://openalex.org/W2107198699","https://openalex.org/W2108035024","https://openalex.org/W2117333383","https://openalex.org/W2117666752","https://openalex.org/W2125014261","https://openalex.org/W2136091400","https://openalex.org/W2142831360","https://openalex.org/W2150286046","https://openalex.org/W2150632173","https://openalex.org/W2155786171","https://openalex.org/W2156277550","https://openalex.org/W2607286972","https://openalex.org/W2793859699","https://openalex.org/W6633466114"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834","https://openalex.org/W657579294"],"abstract_inverted_index":{"The":[0],"proteasome":[1,182],"complex":[2],"is":[3,31,55,229],"the":[4,14,116,137],"main":[5],"responsible":[6],"of":[7,10,16,27,69,118],"proteolytic":[8],"degradation":[9],"cytosolic":[11],"proteins,":[12],"generating":[13],"C-terminus":[15,117,179],"MHC":[17,206,217],"I-restricted":[18],"peptide":[19],"ligands":[20],"and":[21,84,106],"CD8":[22,36,75,120,161],"T":[23,37,121,162],"cell":[24,38,122,163],"epitopes.":[25,39],"Prediction":[26],"proteasomal":[28,49,127,189,226],"cleavage":[29,50,80,134,154,190],"sites":[30,51,135],"thus":[32],"relevant":[33],"for":[34,57,231],"predicting":[35],"We":[40],"previously":[41],"reported":[42],"an":[43],"n-gram":[44],"based":[45],"method":[46,93],"to":[47,78,159,201,209,214,216,223],"predict":[48],"named":[52],"PCPS,":[53],"which":[54,144],"implemented":[56,94,188],"free":[58,232],"public":[59,233],"use":[60,234],"online":[61,235],"at":[62,236],"http://imed.med.ucm.es/pcps/.":[63],"Here,":[64],"we":[65,185],"used":[66,158],"a":[67,91,178,199],"set":[68],"59":[70],"Hepatitis":[71],"C":[72],"Virus":[73],"(HCV)":[74],"T-cell":[76],"epitopes":[77,123,139,164],"analyze":[79],"predictions":[81,156,192],"by":[82,90,165,194,205],"PCPS":[83,99,130,195],"compared":[85],"them":[86],"with":[87,181],"those":[88],"provided":[89,193],"related":[92],"in":[95,103,146,197],"NetChop":[96,102,114],"web":[97],"server.":[98],"clearly":[100],"outperformed":[101],"sensitivity":[104],"(0.88":[105],"0.78,":[107],"respectively);":[108],"it":[109],"identified":[110,131],"much":[111],"better":[112],"than":[113,142],"that":[115,174,220],"tested":[119,138],"likely":[124],"resulted":[125,145],"from":[126,169,225],"cleavage.":[128,227],"However,":[129],"additional":[132],"preferential":[133],"within":[136],"more":[140],"often":[141],"NetChop,":[143],"lower":[147],"specificity":[148],"(0.57":[149],"vs":[150],"0.66,":[151],"respectively).":[152],"Proteasomal":[153],"site":[155,191],"are":[157,221],"enhance":[160],"discarding":[166],"peptides":[167,203,212],"resulting":[168],"peptide-MHC":[170],"I":[171,218],"binding":[172],"models":[173],"do":[175],"not":[176],"have":[177,186],"compatible":[180],"production.":[183],"Thereby,":[184],"now":[187],"n-grams":[196],"RANKPEP,":[198],"tool":[200],"identify":[202],"presented":[204],"molecules,":[207],"allowing":[208],"filter":[210],"out":[211],"predicted":[213],"bind":[215],"molecules":[219],"unlikely":[222],"result":[224],"RANKPEP":[228],"available":[230],"http://imed.med.ucm.es/Tools/rankpep_new.html.":[237]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
