{"id":"https://openalex.org/W3080498684","doi":"https://doi.org/10.1093/bioinformatics/btaa750","title":"DELPHI: accurate deep ensemble model for protein interaction sites prediction","display_name":"DELPHI: accurate deep ensemble model for protein interaction sites prediction","publication_year":2020,"publication_date":"2020-08-19","ids":{"openalex":"https://openalex.org/W3080498684","doi":"https://doi.org/10.1093/bioinformatics/btaa750","mag":"3080498684","pmid":"https://pubmed.ncbi.nlm.nih.gov/32840562"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa750","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa750","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/896/37947501/btaa750.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/37/7/896/37947501/btaa750.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100633406","display_name":"Yiwei Li","orcid":"https://orcid.org/0000-0002-5203-0290"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yiwei Li","raw_affiliation_strings":["Department of Computer Science, The University of Western Ontario London , ON N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Western Ontario London , ON N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047864197","display_name":"G. Brian Golding","orcid":null},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"G Brian Golding","raw_affiliation_strings":["Department of Biology, McMaster University , Hamilton, ON L8S 4K1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, McMaster University , Hamilton, ON L8S 4K1, Canada","institution_ids":["https://openalex.org/I98251732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048178906","display_name":"Lucian Ilie","orcid":"https://orcid.org/0000-0003-1856-3509"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Lucian Ilie","raw_affiliation_strings":["Department of Computer Science, The University of Western Ontario London , ON N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Western Ontario London , ON N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5048178906"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.9207,"has_fulltext":true,"cited_by_count":168,"citation_normalized_percentile":{"value":0.9734718,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"37","issue":"7","first_page":"896","last_page":"904"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4745999872684479,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.4745999872684479,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.27549999952316284,"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":0.08900000154972076,"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":0.743864893913269},{"id":"https://openalex.org/keywords/delphi","display_name":"Delphi","score":0.6492407321929932},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5642712712287903},{"id":"https://openalex.org/keywords/delphi-method","display_name":"Delphi method","score":0.4879309833049774},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.4854060113430023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4826008081436157},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4764159917831421},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.47236496210098267},{"id":"https://openalex.org/keywords/ensemble-forecasting","display_name":"Ensemble forecasting","score":0.46621188521385193},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4338797926902771},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.20144861936569214}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.743864893913269},{"id":"https://openalex.org/C2779495148","wikidata":"https://www.wikidata.org/wiki/Q487378","display_name":"Delphi","level":2,"score":0.6492407321929932},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5642712712287903},{"id":"https://openalex.org/C60641444","wikidata":"https://www.wikidata.org/wiki/Q841602","display_name":"Delphi method","level":2,"score":0.4879309833049774},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.4854060113430023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4826008081436157},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4764159917831421},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47236496210098267},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.46621188521385193},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4338797926902771},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.20144861936569214},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa750","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa750","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/896/37947501/btaa750.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:32840562","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32840562","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/btaa750","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa750","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/7/896/37947501/btaa750.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":[{"display_name":"Life in Land","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3525686075","display_name":null,"funder_award_id":"RGPIN-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320314000","display_name":"Compute Canada","ror":"https://ror.org/03ty8yr27"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3080498684.pdf","grobid_xml":"https://content.openalex.org/works/W3080498684.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1004511050","https://openalex.org/W1019830208","https://openalex.org/W1501531009","https://openalex.org/W1545810434","https://openalex.org/W1569656372","https://openalex.org/W1576278180","https://openalex.org/W1966716734","https://openalex.org/W1975304761","https://openalex.org/W1984712439","https://openalex.org/W1989949705","https://openalex.org/W1993856052","https://openalex.org/W2001457899","https://openalex.org/W2009672036","https://openalex.org/W2009815491","https://openalex.org/W2010890545","https://openalex.org/W2018661561","https://openalex.org/W2026593599","https://openalex.org/W2047544230","https://openalex.org/W2051210555","https://openalex.org/W2054954101","https://openalex.org/W2076052898","https://openalex.org/W2080167197","https://openalex.org/W2097518371","https://openalex.org/W2101234009","https://openalex.org/W2103485392","https://openalex.org/W2109300715","https://openalex.org/W2113985551","https://openalex.org/W2118737745","https://openalex.org/W2124626863","https://openalex.org/W2132926880","https://openalex.org/W2141627824","https://openalex.org/W2144811782","https://openalex.org/W2153153865","https://openalex.org/W2155194485","https://openalex.org/W2156125289","https://openalex.org/W2158714788","https://openalex.org/W2162682281","https://openalex.org/W2166701319","https://openalex.org/W2170747616","https://openalex.org/W2183771695","https://openalex.org/W2192578595","https://openalex.org/W2208315969","https://openalex.org/W2223549968","https://openalex.org/W2264362083","https://openalex.org/W2270702445","https://openalex.org/W2280888683","https://openalex.org/W2335024046","https://openalex.org/W2490420619","https://openalex.org/W2604272474","https://openalex.org/W2618529956","https://openalex.org/W2722005050","https://openalex.org/W2772865572","https://openalex.org/W2898402099","https://openalex.org/W2907063321","https://openalex.org/W2944679105","https://openalex.org/W2952209472","https://openalex.org/W2955690154","https://openalex.org/W2971405760","https://openalex.org/W2975429091","https://openalex.org/W2983201012","https://openalex.org/W2995514860","https://openalex.org/W2998799485","https://openalex.org/W4254751698","https://openalex.org/W6675354045","https://openalex.org/W6678355510"],"related_works":["https://openalex.org/W2062050714","https://openalex.org/W2030487194","https://openalex.org/W2971523465","https://openalex.org/W2031546510","https://openalex.org/W4398393634","https://openalex.org/W1969884608","https://openalex.org/W2041058937","https://openalex.org/W2224226767","https://openalex.org/W2001765788","https://openalex.org/W1573061253"],"abstract_inverted_index":{"MOTIVATION:":[0],"Proteins":[1],"usually":[2],"perform":[3],"their":[4],"functions":[5],"by":[6,147],"interacting":[7],"with":[8,80,129,186,192,230],"other":[9],"proteins,":[10],"which":[11,72],"is":[12,21,161,178,182,209],"why":[13],"accurately":[14],"predicting":[15],"protein-protein":[16],"interaction":[17],"(PPI)":[18],"binding":[19],"sites":[20,55,65,191,201],"a":[22,57,74,77,183],"fundamental":[23],"problem.":[24],"Experimental":[25],"methods":[26,116],"are":[27,34,92,251,260],"slow":[28],"and":[29,76,90,111,139,152,190,215,233,246],"expensive.":[30],"Therefore,":[31],"great":[32],"efforts":[33],"being":[35],"made":[36],"towards":[37],"increasing":[38],"the":[39,114,126,130,134,143,159,166,171,241,247],"performance":[40],"of":[41,50],"computational":[42],"methods.":[43],"RESULTS:":[44],"We":[45,100,155],"propose":[46],"DEep":[47],"Learning":[48],"Prediction":[49],"Highly":[51],"probable":[52],"protein":[53],"Interaction":[54],"(DELPHI),":[56],"new":[58,173],"sequence-based":[59],"deep":[60],"learning":[61],"suite":[62],"for":[63],"PPI-binding":[64],"prediction.":[66],"DELPHI":[67,103,112,176,208,222,242],"has":[68],"an":[69],"ensemble":[70,167],"structure":[71],"combines":[73],"CNN":[75],"RNN":[78],"component":[79],"fine":[81],"tuning":[82],"technique.":[83],"Three":[84],"novel":[85],"features,":[86],"HSP,":[87],"position":[88],"information":[89],"ProtVec":[91],"used":[93],"in":[94,117,235],"addition":[95],"to":[96,104,164],"nine":[97,105],"existing":[98],"ones.":[99],"comprehensively":[101],"compare":[102],"state-of-the-art":[106],"programmes":[107,146],"on":[108],"five":[109],"datasets,":[110],"outperforms":[113],"competing":[115],"all":[118,231],"metrics":[119],"even":[120],"though":[121],"its":[122],"training":[123],"dataset":[124],"shares":[125],"least":[127],"similarities":[128],"testing":[131],"datasets.":[132],"In":[133,196],"most":[135],"important":[136],"metrics,":[137],"AUPRC":[138],"MCC,":[140],"it":[141,177],"surpasses":[142],"second":[144],"best":[145],"as":[148,150,211],"much":[149],"18.5%":[151],"27.7%,":[153],"respectively.":[154],"also":[156],"demonstrated":[157],"that":[158,180],"improvement":[160],"essentially":[162],"due":[163],"using":[165],"model":[168],"and,":[169],"especially,":[170],"three":[172],"features.":[174],"Using":[175],"shown":[179],"there":[181],"strong":[184,193],"correlation":[185],"protein-binding":[187],"residues":[188],"(PBRs)":[189],"evolutionary":[194],"conservation.":[195],"addition,":[197],"DELPHI's":[198],"predicted":[199],"PBR":[200],"closely":[202],"match":[203],"known":[204],"data":[205,259],"from":[206],"Pfam.":[207],"available":[210,253,261],"open-sourced":[212],"standalone":[213,243],"software":[214],"web":[216,223],"server.":[217],"AVAILABILITY":[218],"AND":[219],"IMPLEMENTATION:":[220],"The":[221,238],"server":[224],"can":[225],"be":[226],"found":[227],"at":[228,254,262],"delphi.csd.uwo.ca/,":[229],"datasets":[232],"results":[234],"this":[236],"study.":[237],"trained":[239],"models,":[240],"source":[244],"code,":[245],"feature":[248],"computation":[249],"pipeline":[250],"freely":[252],"github.com/lucian-ilie/DELPHI.":[255],"SUPPLEMENTARY":[256],"INFORMATION:":[257],"Supplementary":[258],"Bioinformatics":[263],"online.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":43},{"year":2024,"cited_by_count":39},{"year":2023,"cited_by_count":31},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":3}],"updated_date":"2026-06-28T08:01:55.173337","created_date":"2025-10-10T00:00:00"}