{"id":"https://openalex.org/W2117299753","doi":"https://doi.org/10.1093/bib/bbr059","title":"A review of statistical methods for prediction of proteolytic cleavage","display_name":"A review of statistical methods for prediction of proteolytic cleavage","publication_year":2011,"publication_date":"2011-12-02","ids":{"openalex":"https://openalex.org/W2117299753","doi":"https://doi.org/10.1093/bib/bbr059","mag":"2117299753","pmid":"https://pubmed.ncbi.nlm.nih.gov/22138323"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr059","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/337/681135/bbr059.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/13/3/337/681135/bbr059.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051564381","display_name":"David A. duVerle","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088032","display_name":"Kyoto Bunkyo University","ror":"https://ror.org/0037an472","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210088032"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"D. A. duVerle","raw_affiliation_strings":["Bioinformatics Center, Kyoto University, Uji, Kyoto 611-0011, Japan. dave@kuicr.kyoto-u.ac.jp","Bioinformatics Center, Kyoto University, Uji, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Kyoto University, Uji, Kyoto 611-0011, Japan. dave@kuicr.kyoto-u.ac.jp","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4210088032"]},{"raw_affiliation_string":"Bioinformatics Center, Kyoto University, Uji, Kyoto 611-0011, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059001924","display_name":"Hiroshi Mamitsuka","orcid":"https://orcid.org/0000-0002-6607-5617"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"H. Mamitsuka","raw_affiliation_strings":["Bioinformatics Center, Kyoto University, Uji, Kyoto 611-0011, Japan","School of Pharmaceutical Sciences at Kyoto University"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Kyoto University, Uji, Kyoto 611-0011, Japan","institution_ids":[]},{"raw_affiliation_string":"School of Pharmaceutical Sciences at Kyoto University","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5051564381"],"corresponding_institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4210088032"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9546,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.73391922,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"3","first_page":"337","last_page":"349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13637","display_name":"Calpain Protease Function and Regulation","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T13637","display_name":"Calpain Protease Function and Regulation","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9984999895095825,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9914000034332275,"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/computer-science","display_name":"Computer science","score":0.6120526790618896},{"id":"https://openalex.org/keywords/cleavage","display_name":"Cleavage (geology)","score":0.6030867695808411},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47099417448043823},{"id":"https://openalex.org/keywords/proteases","display_name":"Proteases","score":0.4627513885498047},{"id":"https://openalex.org/keywords/impossibility","display_name":"Impossibility","score":0.4585859477519989},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2955465316772461},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2447407841682434},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.10587170720100403}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6120526790618896},{"id":"https://openalex.org/C175156509","wikidata":"https://www.wikidata.org/wiki/Q1990218","display_name":"Cleavage (geology)","level":3,"score":0.6030867695808411},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47099417448043823},{"id":"https://openalex.org/C182220744","wikidata":"https://www.wikidata.org/wiki/Q7251226","display_name":"Proteases","level":3,"score":0.4627513885498047},{"id":"https://openalex.org/C2776261394","wikidata":"https://www.wikidata.org/wiki/Q315562","display_name":"Impossibility","level":2,"score":0.4585859477519989},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2955465316772461},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2447407841682434},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.10587170720100403},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C43369102","wikidata":"https://www.wikidata.org/wiki/Q2307625","display_name":"Fracture (geology)","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002154","descriptor_name":"Calpain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002154","descriptor_name":"Calpain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002154","descriptor_name":"Calpain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbr059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr059","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/337/681135/bbr059.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22138323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22138323","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbr059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr059","pdf_url":"https://academic.oup.com/bib/article-pdf/13/3/337/681135/bbr059.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.4300000071525574}],"awards":[],"funders":[{"id":"https://openalex.org/F4320335525","display_name":"Institute for Chemical Research, Kyoto University","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117299753.pdf","grobid_xml":"https://content.openalex.org/works/W2117299753.grobid-xml"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W24553703","https://openalex.org/W1492391409","https://openalex.org/W1514209943","https://openalex.org/W1536886974","https://openalex.org/W1551909886","https://openalex.org/W1555862556","https://openalex.org/W1567730256","https://openalex.org/W1575246003","https://openalex.org/W1587025242","https://openalex.org/W1821507858","https://openalex.org/W1828831131","https://openalex.org/W1912982817","https://openalex.org/W1967501922","https://openalex.org/W1969281238","https://openalex.org/W1970999032","https://openalex.org/W1972245778","https://openalex.org/W1986250049","https://openalex.org/W1987713050","https://openalex.org/W1990376815","https://openalex.org/W1991719291","https://openalex.org/W2002798380","https://openalex.org/W2002832354","https://openalex.org/W2010611103","https://openalex.org/W2012845953","https://openalex.org/W2015936607","https://openalex.org/W2020816856","https://openalex.org/W2024069545","https://openalex.org/W2024993897","https://openalex.org/W2034281860","https://openalex.org/W2041877620","https://openalex.org/W2053604048","https://openalex.org/W2058223738","https://openalex.org/W2074136571","https://openalex.org/W2076015897","https://openalex.org/W2077538414","https://openalex.org/W2083139287","https://openalex.org/W2095249666","https://openalex.org/W2098875971","https://openalex.org/W2099862356","https://openalex.org/W2103496339","https://openalex.org/W2104472920","https://openalex.org/W2105848188","https://openalex.org/W2118185751","https://openalex.org/W2119423166","https://openalex.org/W2119452210","https://openalex.org/W2122460814","https://openalex.org/W2125055259","https://openalex.org/W2133893126","https://openalex.org/W2135214022","https://openalex.org/W2137317896","https://openalex.org/W2138879032","https://openalex.org/W2139492479","https://openalex.org/W2140938836","https://openalex.org/W2148448718","https://openalex.org/W2151831732","https://openalex.org/W2154462399","https://openalex.org/W2156628505","https://openalex.org/W2158001550","https://openalex.org/W2158338599","https://openalex.org/W2160965492","https://openalex.org/W2161381121","https://openalex.org/W2161444669","https://openalex.org/W2165801360","https://openalex.org/W2166486172","https://openalex.org/W2166512255","https://openalex.org/W2168012258","https://openalex.org/W3107101694","https://openalex.org/W4246995357","https://openalex.org/W4320800236"],"related_works":["https://openalex.org/W2973344506","https://openalex.org/W2024010199","https://openalex.org/W2077927848","https://openalex.org/W2400738489","https://openalex.org/W2179790758","https://openalex.org/W1985148152","https://openalex.org/W2701301069","https://openalex.org/W1983518877","https://openalex.org/W2922437993","https://openalex.org/W2766389776"],"abstract_inverted_index":{"A":[0],"fundamental":[1],"component":[2],"of":[3,14,35,42,98,106,127,143,155,189,221,228],"systems":[4],"biology,":[5],"proteolytic":[6,99,166],"cleavage":[7,36,81,134],"is":[8],"involved":[9],"in":[10,133,165],"nearly":[11],"all":[12],"aspects":[13],"cellular":[15],"activities:":[16],"from":[17,192],"gene":[18],"regulation":[19],"to":[20,31,51,74,122,183,198,214,225],"cell":[21],"lifecycle":[22],"regulation.":[23],"Current":[24],"sequencing":[25],"technologies":[26],"have":[27],"made":[28],"it":[29],"possible":[30],"compile":[32],"large":[33],"amount":[34],"data":[37,109,175],"and":[38,79,88,96,131,146,159,174,187,195,208,230],"brought":[39],"greater":[40],"understanding":[41],"the":[43,48,62,94,104,128,185],"underlying":[44],"protein":[45],"interactions.":[46],"However,":[47],"practical":[49],"impossibility":[50],"exhaustively":[52],"retrieve":[53],"substrate":[54,77],"sequences":[55],"through":[56],"experimentation":[57],"alone":[58],"has":[59],"long":[60],"highlighted":[61],"need":[63],"for":[64,83,169,172,179,218],"efficient":[65],"computational":[66],"prediction":[67,135],"methods.":[68,234],"Such":[69],"methods":[70,87,136,202],"must":[71],"be":[72],"able":[73],"quickly":[75],"mark":[76],"candidates":[78],"putative":[80],"sites":[82],"further":[84],"analysis.":[85],"Available":[86],"expected":[89],"reliability":[90],"depend":[91],"heavily":[92],"on":[93,151],"type":[95],"complexity":[97],"action,":[100],"as":[101,103,204],"well":[102],"availability":[105,176],"well-labelled":[107],"experimental":[108],"sets:":[110],"factors":[111],"varying":[112],"greatly":[113],"across":[114,233],"enzyme":[115],"families.":[116],"For":[117],"this":[118],"review,":[119],"we":[120,181,223],"chose":[121],"give":[123],"a":[124,139,149,215],"quick":[125],"overview":[126,217],"general":[129],"issues":[130],"challenges":[132],"followed":[137],"by":[138],"more":[140,199],"in-depth":[141],"presentation":[142],"major":[144],"techniques":[145,190],"implementations,":[147],"with":[148],"focus":[150],"two":[152],"particular":[153],"families":[154],"cysteine":[156],"proteases:":[157],"caspases":[158],"calpains.":[160],"Through":[161],"their":[162],"respective":[163],"differences":[164],"specificity":[167],"(high":[168],"caspases,":[170],"broader":[171],"calpains)":[173],"(much":[177],"lower":[178],"calpains),":[180],"aimed":[182],"illustrate":[184],"strengths":[186],"limitations":[188],"ranging":[191],"position-based":[193],"matrices":[194],"decision":[196],"trees":[197],"flexible":[200],"machine-learning":[201],"such":[203],"hidden":[205],"Markov":[206],"models":[207],"Support":[209],"Vector":[210],"Machines.":[211],"In":[212],"addition":[213],"technical":[216],"each":[219],"family":[220],"algorithms,":[222],"tried":[224],"provide":[226],"elements":[227],"evaluation":[229],"performance":[231],"comparison":[232]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
