{"id":"https://openalex.org/W2883972651","doi":"https://doi.org/10.1093/bioinformatics/bty667","title":"WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source","display_name":"WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source","publication_year":2018,"publication_date":"2018-07-24","ids":{"openalex":"https://openalex.org/W2883972651","doi":"https://doi.org/10.1093/bioinformatics/bty667","mag":"2883972651","pmid":"https://pubmed.ncbi.nlm.nih.gov/30052776"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty667","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty667","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5049726166","display_name":"Tatiana Radchenko","orcid":"https://orcid.org/0000-0003-4962-7229"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Tatiana Radchenko","raw_affiliation_strings":["Lead Molecular Design, S.L., Sant Cugat del Vall\u00e9s, Spain","Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-4962-7229","affiliations":[{"raw_affiliation_string":"Lead Molecular Design, S.L., Sant Cugat del Vall\u00e9s, Spain","institution_ids":[]},{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000543257","display_name":"Fabien Fontaine","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fabien Fontaine","raw_affiliation_strings":["Lead Molecular Design, S.L., Sant Cugat del Vall\u00e9s, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lead Molecular Design, S.L., Sant Cugat del Vall\u00e9s, Spain","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040612055","display_name":"Luca Morettoni","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luca Morettoni","raw_affiliation_strings":["Molecular Discovery Ltd, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Discovery Ltd, London, UK","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088064237","display_name":"Ismael Zamora","orcid":"https://orcid.org/0000-0002-7700-0354"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Ismael Zamora","raw_affiliation_strings":["Lead Molecular Design, S.L., Sant Cugat del Vall\u00e9s, Spain","Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lead Molecular Design, S.L., Sant Cugat del Vall\u00e9s, Spain","institution_ids":[]},{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5049726166","https://openalex.org/A5088064237"],"corresponding_institution_ids":["https://openalex.org/I170486558"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1649,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.48412007,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"35","issue":"4","first_page":"650","last_page":"655"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.47519999742507935,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.47519999742507935,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.18080000579357147,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.053700000047683716,"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/cleavage","display_name":"Cleavage (geology)","score":0.7462571263313293},{"id":"https://openalex.org/keywords/peptide-bond","display_name":"Peptide bond","score":0.6747879981994629},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.6633452773094177},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5997816324234009},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5380949378013611},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.5365007519721985},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5116186738014221},{"id":"https://openalex.org/keywords/amide","display_name":"Amide","score":0.5101635456085205},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.4824267327785492},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4649200737476349},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43250128626823425},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.4251844584941864},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.386495441198349},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3656378388404846},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.25442519783973694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20684021711349487},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18356075882911682},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12641894817352295}],"concepts":[{"id":"https://openalex.org/C175156509","wikidata":"https://www.wikidata.org/wiki/Q1990218","display_name":"Cleavage (geology)","level":3,"score":0.7462571263313293},{"id":"https://openalex.org/C31684184","wikidata":"https://www.wikidata.org/wiki/Q33293","display_name":"Peptide bond","level":3,"score":0.6747879981994629},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.6633452773094177},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5997816324234009},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5380949378013611},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.5365007519721985},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5116186738014221},{"id":"https://openalex.org/C2778439535","wikidata":"https://www.wikidata.org/wiki/Q188777","display_name":"Amide","level":2,"score":0.5101635456085205},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.4824267327785492},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4649200737476349},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43250128626823425},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.4251844584941864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.386495441198349},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3656378388404846},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.25442519783973694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20684021711349487},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18356075882911682},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12641894817352295},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty667","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty667","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30052776","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30052776","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W569561726","https://openalex.org/W1860382351","https://openalex.org/W1953569147","https://openalex.org/W1970724938","https://openalex.org/W1977219317","https://openalex.org/W1985469117","https://openalex.org/W1985917720","https://openalex.org/W2000034207","https://openalex.org/W2011201847","https://openalex.org/W2050000500","https://openalex.org/W2055586791","https://openalex.org/W2080653934","https://openalex.org/W2084251502","https://openalex.org/W2084934285","https://openalex.org/W2090636474","https://openalex.org/W2092236356","https://openalex.org/W2093656309","https://openalex.org/W2094120651","https://openalex.org/W2116209691","https://openalex.org/W2137450588","https://openalex.org/W2149746810","https://openalex.org/W2152365098","https://openalex.org/W2160549654","https://openalex.org/W2204075485","https://openalex.org/W2327675006","https://openalex.org/W2411646172","https://openalex.org/W2724823461","https://openalex.org/W2766389776","https://openalex.org/W2767059855","https://openalex.org/W4254911074"],"related_works":["https://openalex.org/W2914310478","https://openalex.org/W2003068062","https://openalex.org/W2301966358","https://openalex.org/W1964001288","https://openalex.org/W2050312203","https://openalex.org/W2465933703","https://openalex.org/W2809149148","https://openalex.org/W1929109117","https://openalex.org/W2548072374","https://openalex.org/W2030328557"],"abstract_inverted_index":{"SUMMARY:":[0],"More":[1],"than":[2],"150":[3],"peptide":[4,31,91],"therapeutics":[5],"are":[6,195],"globally":[7],"in":[8,24,58,142,176],"clinical":[9],"development.":[10],"Many":[11],"enzymatic":[12],"barriers":[13],"should":[14],"be":[15,22,34,148],"crossed":[16],"by":[17,103,119],"a":[18,26,52,85,96,126,133,152,178],"successful":[19],"drug":[20],"to":[21,41,47,110,150,155],"prosperous":[23],"such":[25,77,177],"process.":[27],"Therefore,":[28],"the":[29,37,43,64,79,111,139,143,157,169,172,181],"new":[30,53],"drugs":[32],"must":[33],"designed":[35],"preventing":[36],"potential":[38],"protease":[39,48],"cleavage":[40,160],"make":[42],"compound":[44],"less":[45],"susceptible":[46],"reaction.":[49],"We":[50],"present":[51],"data":[54,72,194],"analysis":[55,154],"tool":[56,83],"developed":[57],"WebMetabase,":[59],"an":[60],"approach":[61],"that":[62,129,174],"stores":[63],"information":[65],"from":[66,74],"liquid":[67],"chromatography":[68],"mass":[69],"spectrometry-based":[70],"experimental":[71],"or":[73],"external":[75],"sources":[76],"as":[78,95],"MEROPS":[80],"database.":[81,144,186],"The":[82],"is":[84,93,117],"chemically":[86],"aware":[87],"system":[88],"where":[89],"each":[90,136],"substrate":[92],"presented":[94],"sequence":[97],"of":[98,138,171],"structural":[99],"blocks":[100],"(SBs)":[101],"connected":[102],"amide":[104,164],"bonds":[105],"and":[106,122,135],"not":[107],"being":[108],"limited":[109],"natural":[112],"amino":[113],"acids.":[114],"Each":[115],"SB":[116,134,173],"characterized":[118],"its":[120],"pharmacophoric":[121],"physicochemical":[123],"properties":[124],"including":[125],"similarity":[127,170],"score":[128],"describes":[130],"likelihood":[131],"between":[132],"one":[137],"other":[140],"SBs":[141],"This":[145],"methodology":[146],"can":[147],"used":[149],"perform":[151],"frequency":[153],"discover":[156],"most":[158],"frequent":[159],"sites":[161],"for":[162],"similar":[163],"bonds,":[165],"defined":[166],"based":[167],"on":[168],"participate":[175],"bond":[179],"within":[180],"experimentally":[182],"derived":[183],"and/or":[184],"public":[185],"AVAILABILITY":[187],"AND":[188],"IMPLEMENTATION:":[189],"http://webmetabase.com:8182/WebMetabaseBioinformatics/.":[190],"SUPPLEMENTARY":[191],"INFORMATION:":[192],"Supplementary":[193],"available":[196],"at":[197],"Bioinformatics":[198],"online.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
