{"id":"https://openalex.org/W2563500611","doi":"https://doi.org/10.1093/bioinformatics/btw792","title":"PhosD: inferring kinase\u2013substrate interactions based on protein domains","display_name":"PhosD: inferring kinase\u2013substrate interactions based on protein domains","publication_year":2016,"publication_date":"2016-12-09","ids":{"openalex":"https://openalex.org/W2563500611","doi":"https://doi.org/10.1093/bioinformatics/btw792","mag":"2563500611","pmid":"https://pubmed.ncbi.nlm.nih.gov/28031187"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw792","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw792","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1197/25150370/btw792.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1197/25150370/btw792.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086370741","display_name":"Guimin Qin","orcid":"https://orcid.org/0000-0001-8272-9599"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gui-Min Qin","raw_affiliation_strings":["School of Electronics and Information Engineering, Tongji University, Shanghai, China","School of Software, Xidian University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronics and Information Engineering, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Software, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068852522","display_name":"Ruiyi Li","orcid":"https://orcid.org/0000-0002-6414-4834"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui-Yi Li","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049435754","display_name":"Xing\u2010Ming Zhao","orcid":"https://orcid.org/0000-0002-4531-3970"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xing-Ming Zhao","raw_affiliation_strings":["School of Electronics and Information Engineering, Tongji University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronics and Information Engineering, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049435754"],"corresponding_institution_ids":["https://openalex.org/I116953780"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8543,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.77062216,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"8","first_page":"1197","last_page":"1204"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7971000075340271,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7971000075340271,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.06390000134706497,"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":0.03889999911189079,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5545071959495544},{"id":"https://openalex.org/keywords/substrate-specificity","display_name":"Substrate specificity","score":0.5398025512695312},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5293586850166321},{"id":"https://openalex.org/keywords/substrate","display_name":"Substrate (aquarium)","score":0.5159890651702881},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3078416585922241},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2775341868400574},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24160873889923096},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.09676375985145569}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5545071959495544},{"id":"https://openalex.org/C2994592520","wikidata":"https://www.wikidata.org/wiki/Q5090496","display_name":"Substrate specificity","level":3,"score":0.5398025512695312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5293586850166321},{"id":"https://openalex.org/C2777289219","wikidata":"https://www.wikidata.org/wiki/Q7632154","display_name":"Substrate (aquarium)","level":2,"score":0.5159890651702881},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3078416585922241},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2775341868400574},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24160873889923096},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.09676375985145569},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw792","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw792","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1197/25150370/btw792.pdf","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:28031187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28031187","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":{"id":"doi:10.1093/bioinformatics/btw792","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw792","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1197/25150370/btw792.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1078840120","display_name":null,"funder_award_id":"JB151005","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2576084723","display_name":null,"funder_award_id":"61602347","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5369175185","display_name":"\u57fa\u4e8e\u591a\u7ec4\u5b66\u6570\u636e\u6574\u5408\u7684\u75be\u75c5\u57fa\u56e0\u9884\u6d4b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61572363","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6773893820","display_name":null,"funder_award_id":"BDZ011401","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8179239958","display_name":null,"funder_award_id":"91530321","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W50100400","https://openalex.org/W1570643690","https://openalex.org/W1791902585","https://openalex.org/W1971727526","https://openalex.org/W1988520084","https://openalex.org/W1993450321","https://openalex.org/W1995540460","https://openalex.org/W1995989434","https://openalex.org/W2003079893","https://openalex.org/W2007114641","https://openalex.org/W2031028006","https://openalex.org/W2037442572","https://openalex.org/W2038492487","https://openalex.org/W2039577125","https://openalex.org/W2040683679","https://openalex.org/W2043274355","https://openalex.org/W2056499061","https://openalex.org/W2057545775","https://openalex.org/W2075184904","https://openalex.org/W2075490509","https://openalex.org/W2090076432","https://openalex.org/W2095492902","https://openalex.org/W2097698606","https://openalex.org/W2104726963","https://openalex.org/W2105869859","https://openalex.org/W2110095004","https://openalex.org/W2122863289","https://openalex.org/W2128330762","https://openalex.org/W2130253098","https://openalex.org/W2130775057","https://openalex.org/W2132582966","https://openalex.org/W2136179119","https://openalex.org/W2140638448","https://openalex.org/W2140961919","https://openalex.org/W2146913682","https://openalex.org/W2151031196","https://openalex.org/W2154727263","https://openalex.org/W2155239883","https://openalex.org/W2155898507","https://openalex.org/W2156916536","https://openalex.org/W2158590514","https://openalex.org/W2159482845","https://openalex.org/W2164461702","https://openalex.org/W2165425526","https://openalex.org/W2257018217","https://openalex.org/W2316947589","https://openalex.org/W2333525116","https://openalex.org/W2337819340","https://openalex.org/W2345065869","https://openalex.org/W2915975108","https://openalex.org/W2916483810","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2117340465","https://openalex.org/W2046536786","https://openalex.org/W1981911623","https://openalex.org/W2587733587"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"the":[2,9,47,50,80,124,137,143,145,154,182],"kinase-substrate":[3,48,73,83,116,158],"relationships":[4,74,117],"is":[5,30],"vital":[6],"to":[7,45,55,71,162],"understanding":[8],"phosphorylation":[10,23],"events":[11],"and":[12,153,189],"various":[13],"biological":[14],"processes,":[15],"especially":[16],"signal":[17],"transductions.":[18],"Although":[19],"large":[20],"amount":[21],"of":[22,113,127],"sites":[24],"have":[25,42],"been":[26,43],"detected,":[27],"unfortunately,":[28],"it":[29],"rarely":[31],"known":[32,141],"which":[33],"kinases":[34],"activate":[35],"those":[36],"sites.":[37],"Despite":[38],"distinct":[39],"computational":[40,179],"approaches":[41,102,180],"proposed":[44],"predict":[46,72],"interactions,":[49,96],"prediction":[51],"accuracy":[52],"still":[53],"needs":[54],"be":[56,163],"improved.":[57],"RESULTS:":[58],"In":[59,110],"this":[60],"paper,":[61],"we":[62,131],"propose":[63],"a":[64,135],"novel":[65],"probabilistic":[66],"model":[67],"named":[68],"as":[69],"PhosD":[70,98],"based":[75],"on":[76,103],"protein":[77],"domains":[78,155],"with":[79,87,107],"assumption":[81],"that":[82,133],"interactions":[84,159],"are":[85,118,140,160,191,201],"accomplished":[86],"kinase-domain":[88],"interactions.":[89],"By":[90],"further":[91],"taking":[92],"into":[93],"account":[94],"protein-protein":[95],"our":[97,114,128],"outperforms":[99],"other":[100],"popular":[101],"several":[104],"benchmark":[105],"datasets":[106],"higher":[108],"precision.":[109],"addition,":[111],"some":[112],"predicted":[115,149],"validated":[119],"by":[120,169],"signaling":[121],"pathways,":[122],"indicating":[123],"predictive":[125],"power":[126],"approach.":[129],"Furthermore,":[130],"notice":[132],"given":[134],"kinase,":[136],"more":[138,146,164,177],"substrates":[139,150],"for":[142],"kinase":[144],"accurate":[147],"its":[148],"will":[151],"be,":[152],"involved":[156],"in":[157,181],"found":[161],"conserved":[165],"across":[166],"proteins":[167],"phosphorylated":[168],"multiple":[170],"kinases.":[171],"These":[172],"findings":[173],"can":[174],"help":[175],"develop":[176],"efficient":[178],"future.":[183],"AVAILABILITY":[184],"AND":[185],"IMPLEMENTATION:":[186],"The":[187],"data":[188,200],"results":[190],"available":[192,202],"at":[193,203],"http://comp-sysbio.org/phosd.":[194],"CONTACT:":[195],"xm_zhao@tongji.edu.cn.":[196],"SUPPLEMENTARY":[197],"INFORMATION:":[198],"Supplementary":[199],"Bioinformatics":[204],"online.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
