{"id":"https://openalex.org/W4319294199","doi":"https://doi.org/10.1021/acs.jcim.2c01413","title":"SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein\u2013Ligand-Binding Sites","display_name":"SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein\u2013Ligand-Binding Sites","publication_year":2023,"publication_date":"2023-02-06","ids":{"openalex":"https://openalex.org/W4319294199","doi":"https://doi.org/10.1021/acs.jcim.2c01413","pmid":"https://pubmed.ncbi.nlm.nih.gov/36744300"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01413","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01413","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/A5084192743","display_name":"Sergei Evteev","orcid":"https://orcid.org/0000-0003-2179-3508"},"institutions":[{"id":"https://openalex.org/I4210106534","display_name":"All Russia Research Institute of Automatics","ror":"https://ror.org/01kp4cp54","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1296541250","https://openalex.org/I4210106534"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Sergei A. Evteev","raw_affiliation_strings":["The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia"],"raw_orcid":"https://orcid.org/0000-0003-2179-3508","affiliations":[{"raw_affiliation_string":"The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia","institution_ids":["https://openalex.org/I4210106534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029899222","display_name":"Alexey Ereshchenko","orcid":"https://orcid.org/0000-0002-7435-5643"},"institutions":[{"id":"https://openalex.org/I4210106534","display_name":"All Russia Research Institute of Automatics","ror":"https://ror.org/01kp4cp54","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1296541250","https://openalex.org/I4210106534"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexey V. Ereshchenko","raw_affiliation_strings":["The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia","institution_ids":["https://openalex.org/I4210106534"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011234875","display_name":"Yan A. Ivanenkov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210106534","display_name":"All Russia Research Institute of Automatics","ror":"https://ror.org/01kp4cp54","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1296541250","https://openalex.org/I4210106534"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Yan A. Ivanenkov","raw_affiliation_strings":["The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Federal State Unitary Enterprise Dukhov Automatics Research Institute, Moscow 127055, Russia","institution_ids":["https://openalex.org/I4210106534"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5084192743"],"corresponding_institution_ids":["https://openalex.org/I4210106534"],"apc_list":null,"apc_paid":null,"fwci":4.8494,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.95877589,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"63","issue":"4","first_page":"1124","last_page":"1132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9976000189781189,"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/graph","display_name":"Graph","score":0.6218163371086121},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5818948745727539},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4800218641757965},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4266390800476074},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41180670261383057},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3440987765789032},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.23541826009750366},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19604459404945374}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6218163371086121},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5818948745727539},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4800218641757965},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4266390800476074},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41180670261383057},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3440987765789032},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.23541826009750366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19604459404945374}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c01413","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01413","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:36744300","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36744300","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":[{"score":0.5299999713897705,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1971618381","https://openalex.org/W1976229976","https://openalex.org/W1980969309","https://openalex.org/W1984563996","https://openalex.org/W2002368219","https://openalex.org/W2044703506","https://openalex.org/W2058107061","https://openalex.org/W2066143642","https://openalex.org/W2067191022","https://openalex.org/W2070927843","https://openalex.org/W2114850508","https://openalex.org/W2130479394","https://openalex.org/W2139362074","https://openalex.org/W2143117875","https://openalex.org/W2157760740","https://openalex.org/W2164088236","https://openalex.org/W2171180835","https://openalex.org/W2171323225","https://openalex.org/W2506658812","https://openalex.org/W2567231876","https://openalex.org/W2617750324","https://openalex.org/W2622009965","https://openalex.org/W2767812299","https://openalex.org/W2799327292","https://openalex.org/W2808147451","https://openalex.org/W3003257820","https://openalex.org/W3012511738","https://openalex.org/W3097054638","https://openalex.org/W3100043476","https://openalex.org/W3183967699","https://openalex.org/W3187966659","https://openalex.org/W3197082762","https://openalex.org/W4237142329","https://openalex.org/W4285081903"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3209574120","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Identifying":[0],"ligand-binding":[1,106],"sites":[2,55,107],"on":[3],"the":[4,12,28,110],"protein":[5],"surface":[6],"is":[7,42],"a":[8,44,68,79,130],"crucial":[9],"step":[10],"in":[11,86],"structure-based":[13],"drug":[14,62,139],"design.":[15,63,140],"Although":[16],"multiple":[17],"techniques":[18],"have":[19],"been":[20],"proposed,":[21],"including":[22],"those":[23],"using":[24],"machine":[25],"learning":[26,38],"algorithms,":[27],"existing":[29],"solutions":[30],"do":[31],"not":[32],"provide":[33],"significant":[34],"advantages":[35],"over":[36],"nonmachine":[37],"approaches":[39,58],"and":[40,93,116],"there":[41],"still":[43],"big":[45],"room":[46],"for":[47,71,133,137],"improvement.":[48],"The":[49],"low":[50],"ability":[51,98],"to":[52,60,77,99,102,109],"identify":[53],"protein-ligand-binding":[54],"makes":[56],"available":[57],"inapplicable":[59],"automated":[61,138],"Here,":[64],"we":[65],"present":[66],"SiteRadar,":[67],"new":[69],"algorithm":[70],"mapping":[72],"cavities":[73],"that":[74],"are":[75],"likely":[76],"bind":[78],"small-molecule":[80],"ligand.":[81],"SiteRadar":[82,95,125],"shows":[83],"higher":[84],"accuracy":[85],"binding":[87],"site":[88],"identification":[89],"compared":[90],"with":[91],"FPocket":[92],"PUResNet.":[94],"demonstrates":[96],"an":[97],"detect":[100],"up":[101],"74%":[103],"of":[104,121],"true":[105],"according":[108],"top":[111],"N":[112],"+":[113],"2":[114],"metric":[115],"usually":[117],"covers":[118],"approximately":[119],"80%":[120],"ligand":[122],"atoms.":[123],"Therefore,":[124],"can":[126],"be":[127],"regarded":[128],"as":[129],"promising":[131],"solution":[132],"implementation":[134],"into":[135],"algorithms":[136]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}