{"id":"https://openalex.org/W3209421341","doi":"https://doi.org/10.1021/acs.jcim.1c01135","title":"pdCSM-PPI: Using Graph-Based Signatures to Identify Protein\u2013Protein Interaction Inhibitors","display_name":"pdCSM-PPI: Using Graph-Based Signatures to Identify Protein\u2013Protein Interaction Inhibitors","publication_year":2021,"publication_date":"2021-11-01","ids":{"openalex":"https://openalex.org/W3209421341","doi":"https://doi.org/10.1021/acs.jcim.1c01135","mag":"3209421341","pmid":"https://pubmed.ncbi.nlm.nih.gov/34719929"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c01135","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01135","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5001797627","display_name":"Carlos H. M. Rodrigues","orcid":"https://orcid.org/0000-0002-4420-6401"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Carlos H. M. Rodrigues","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071950872","display_name":"Douglas E. V. Pires","orcid":"https://orcid.org/0000-0002-3004-2119"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Douglas E. V. Pires","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia","School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091903225","display_name":"David B. Ascher","orcid":"https://orcid.org/0000-0003-2948-2413"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"David B. Ascher","raw_affiliation_strings":["Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia","Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071950872","https://openalex.org/A5091903225"],"corresponding_institution_ids":["https://openalex.org/I142471025","https://openalex.org/I165143802","https://openalex.org/I165779595"],"apc_list":null,"apc_paid":null,"fwci":4.5204,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.9509677,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"61","issue":"11","first_page":"5438","last_page":"5445"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9965000152587891,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9965000152587891,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9825000166893005,"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/T11440","display_name":"Click Chemistry and Applications","score":0.9254000186920166,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49919891357421875},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4983687400817871},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46205583214759827},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40938982367515564},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40282562375068665},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24940189719200134},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18993332982063293},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.126886785030365}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49919891357421875},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4983687400817871},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46205583214759827},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40938982367515564},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40282562375068665},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24940189719200134},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18993332982063293},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.126886785030365}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c01135","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01135","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:34719929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34719929","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6454673195","display_name":null,"funder_award_id":"GNT1174405","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320322858","display_name":"State Government of Victoria","ror":"https://ror.org/02xvc5r05"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320334711","display_name":"Melbourne Research, University of Melbourne","ror":"https://ror.org/01ej9dk98"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1852608922","https://openalex.org/W1935098740","https://openalex.org/W1979814868","https://openalex.org/W1984452172","https://openalex.org/W1986522554","https://openalex.org/W2009867031","https://openalex.org/W2018745394","https://openalex.org/W2030071974","https://openalex.org/W2040074453","https://openalex.org/W2064488723","https://openalex.org/W2074964005","https://openalex.org/W2083441741","https://openalex.org/W2096679774","https://openalex.org/W2101234009","https://openalex.org/W2103459989","https://openalex.org/W2119316461","https://openalex.org/W2121666644","https://openalex.org/W2123400824","https://openalex.org/W2127432713","https://openalex.org/W2128247932","https://openalex.org/W2137801157","https://openalex.org/W2143426320","https://openalex.org/W2146208101","https://openalex.org/W2318657222","https://openalex.org/W2331480251","https://openalex.org/W2338762894","https://openalex.org/W2400041270","https://openalex.org/W2415933611","https://openalex.org/W2606696614","https://openalex.org/W2743857398","https://openalex.org/W2779144909","https://openalex.org/W2794913173","https://openalex.org/W2801491392","https://openalex.org/W2900090807","https://openalex.org/W2945403072","https://openalex.org/W2972499938","https://openalex.org/W2980372463","https://openalex.org/W2982575658","https://openalex.org/W3026328277","https://openalex.org/W3038264863","https://openalex.org/W3083008290","https://openalex.org/W3097145107","https://openalex.org/W3118960334","https://openalex.org/W3154108572","https://openalex.org/W4234326582","https://openalex.org/W4376453232"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2099982459","https://openalex.org/W2109298101","https://openalex.org/W2007507741","https://openalex.org/W2159860826","https://openalex.org/W3192210502","https://openalex.org/W1981737222","https://openalex.org/W1569394480"],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1,22],"are":[2],"promising":[3],"sites":[4],"for":[5],"development":[6],"of":[7,37,52,58,125,147,153,172],"selective":[8],"drugs;":[9],"however,":[10],"they":[11],"have":[12],"generally":[13],"been":[14],"viewed":[15],"as":[16,180],"challenging":[17],"targets.":[18,72],"Molecules":[19],"targeting":[20],"protein-protein":[21,61,112],"tend":[23],"to":[24,55,68,80,91,97,137,166],"be":[25,162],"larger":[26],"and":[27,87,93,149,151,155,185],"more":[28,169],"lipophilic":[29],"than":[30],"other":[31],"drug-like":[32],"molecules,":[33],"mimicking":[34],"the":[35],"properties":[36],"interacting":[38],"interfaces.":[39],"Here,":[40],"we":[41,108,134],"propose":[42],"a":[43,49,110,122,128],"machine":[44],"learning":[45],"approach":[46,65],"that":[47,77],"uses":[48],"graph-based":[50],"representation":[51],"small":[53],"molecules":[54],"guide":[56,168],"identification":[57],"inhibitors":[59],"modulating":[60],"interactions,":[62],"pdCSM-PPI.":[63],"This":[64],"was":[66],"applied":[67],"21":[69],"different":[70],"PPI":[71,174],"We":[73,158],"developed":[74,109],"interaction-specific":[75],"models":[76],"were":[78,135],"able":[79,136],"accurately":[81,118,138],"identify":[82,139],"active":[83,140],"compounds":[84],"achieving":[85,144],"MCC":[86],"F1":[88],"scores":[89],"up":[90,96],"1,":[92],"Pearson's":[94,123],"correlations":[95],"0.87,":[98],"outperforming":[99],"previous":[100],"approaches.":[101],"Using":[102],"insights":[103],"from":[104,141],"these":[105],"individual":[106],"models,":[107],"generic":[111],"interaction":[113],"modulator":[114],"predictive":[115],"model,":[116],"which":[117],"predicted":[119],"IC50":[120],"with":[121],"correlation":[124],"0.64":[126],"on":[127],"low":[129],"redundancy":[130],"blind":[131],"test.":[132],"Importantly,":[133],"inactive":[142],"compounds,":[143],"an":[145,163,181],"AUC":[146],"0.77":[148],"sensitivity":[150],"specificity":[152],"76%":[154],"78%,":[156],"respectively.":[157],"believe":[159],"pdCSM-PPI":[160],"will":[161],"important":[164],"tool":[165],"help":[167],"efficient":[170],"screening":[171],"new":[173],"inhibitors;":[175],"it":[176],"is":[177],"freely":[178],"available":[179],"easy-to-use":[182],"web":[183],"server":[184],"API":[186],"at":[187],"http://biosig.unimelb.edu.au/pdcsm_ppi.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":4}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}