{"id":"https://openalex.org/W4396844630","doi":"https://doi.org/10.1002/aisy.202400238","title":"ClassyPose: A Machine\u2010Learning Classification Model for Ligand Pose Selection Applied to Virtual Screening in Drug Discovery","display_name":"ClassyPose: A Machine\u2010Learning Classification Model for Ligand Pose Selection Applied to Virtual Screening in Drug Discovery","publication_year":2024,"publication_date":"2024-05-12","ids":{"openalex":"https://openalex.org/W4396844630","doi":"https://doi.org/10.1002/aisy.202400238"},"language":"en","primary_location":{"id":"doi:10.1002/aisy.202400238","is_oa":true,"landing_page_url":"https://doi.org/10.1002/aisy.202400238","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/aisy.202400238","source":{"id":"https://openalex.org/S4210212817","display_name":"Advanced Intelligent Systems","issn_l":"2640-4567","issn":["2640-4567"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advanced Intelligent Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/aisy.202400238","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014611705","display_name":"Viet\u2010Khoa Tran\u2010Nguyen","orcid":"https://orcid.org/0000-0001-7497-333X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Viet\u2010Khoa Tran\u2010Nguyen","raw_affiliation_strings":["Unit\u00e9 de Biologie Fonctionnelle et Adaptative Universit\u00e9 Paris Cit\u00e9, CNRS UMR8251, INSERM U1133  Paris F\u201075013 France"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 de Biologie Fonctionnelle et Adaptative Universit\u00e9 Paris Cit\u00e9, CNRS UMR8251, INSERM U1133  Paris F\u201075013 France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015097541","display_name":"Anne\u2010Claude Camproux","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne\u2010Claude Camproux","raw_affiliation_strings":["Unit\u00e9 de Biologie Fonctionnelle et Adaptative Universit\u00e9 Paris Cit\u00e9, CNRS UMR8251, INSERM U1133  Paris F\u201075013 France"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 de Biologie Fonctionnelle et Adaptative Universit\u00e9 Paris Cit\u00e9, CNRS UMR8251, INSERM U1133  Paris F\u201075013 France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005294445","display_name":"Olivier Taboureau","orcid":"https://orcid.org/0000-0001-7081-2491"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Olivier Taboureau","raw_affiliation_strings":["Unit\u00e9 de Biologie Fonctionnelle et Adaptative Universit\u00e9 Paris Cit\u00e9, CNRS UMR8251, INSERM U1133  Paris F\u201075013 France"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 de Biologie Fonctionnelle et Adaptative Universit\u00e9 Paris Cit\u00e9, CNRS UMR8251, INSERM U1133  Paris F\u201075013 France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005294445","https://openalex.org/A5014611705"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I204730241"],"apc_list":{"value":2750,"currency":"USD","value_usd":2750},"apc_paid":{"value":2750,"currency":"USD","value_usd":2750},"fwci":2.1701,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.88211255,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9652000069618225,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9642000198364258,"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/virtual-screening","display_name":"Virtual screening","score":0.8869645595550537},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6553534269332886},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6308541297912598},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.6099977493286133},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.609430193901062},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.594207763671875},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.5483610033988953},{"id":"https://openalex.org/keywords/pose","display_name":"Pose","score":0.42670533061027527},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4165959060192108},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21667993068695068},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09265574812889099},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07495081424713135}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8869645595550537},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6553534269332886},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6308541297912598},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.6099977493286133},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.609430193901062},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.594207763671875},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.5483610033988953},{"id":"https://openalex.org/C52102323","wikidata":"https://www.wikidata.org/wiki/Q1671968","display_name":"Pose","level":2,"score":0.42670533061027527},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4165959060192108},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21667993068695068},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09265574812889099},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07495081424713135},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1002/aisy.202400238","is_oa":true,"landing_page_url":"https://doi.org/10.1002/aisy.202400238","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/aisy.202400238","source":{"id":"https://openalex.org/S4210212817","display_name":"Advanced Intelligent Systems","issn_l":"2640-4567","issn":["2640-4567"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advanced Intelligent Systems","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:17e6e3bb60fe4495a264c69ca657ec89","is_oa":true,"landing_page_url":"https://doaj.org/article/17e6e3bb60fe4495a264c69ca657ec89","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Advanced Intelligent Systems, Vol 6, Iss 12, Pp n/a-n/a (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1002/aisy.202400238","is_oa":true,"landing_page_url":"https://doi.org/10.1002/aisy.202400238","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/aisy.202400238","source":{"id":"https://openalex.org/S4210212817","display_name":"Advanced Intelligent Systems","issn_l":"2640-4567","issn":["2640-4567"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advanced Intelligent Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.46000000834465027}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396844630.pdf"},"referenced_works_count":124,"referenced_works":["https://openalex.org/W572249369","https://openalex.org/W1513150088","https://openalex.org/W1570758308","https://openalex.org/W1592950931","https://openalex.org/W1925334442","https://openalex.org/W1950993160","https://openalex.org/W1968319881","https://openalex.org/W1973499863","https://openalex.org/W1975898379","https://openalex.org/W1983194490","https://openalex.org/W1985300726","https://openalex.org/W1988037271","https://openalex.org/W1993285168","https://openalex.org/W2001722230","https://openalex.org/W2007066406","https://openalex.org/W2016381774","https://openalex.org/W2017663720","https://openalex.org/W2022214219","https://openalex.org/W2022998385","https://openalex.org/W2024060531","https://openalex.org/W2028629022","https://openalex.org/W2030286884","https://openalex.org/W2032233064","https://openalex.org/W2034419650","https://openalex.org/W2038542598","https://openalex.org/W2040990879","https://openalex.org/W2059464558","https://openalex.org/W2067455153","https://openalex.org/W2070405735","https://openalex.org/W2071557543","https://openalex.org/W2072886335","https://openalex.org/W2075020622","https://openalex.org/W2075186867","https://openalex.org/W2079331631","https://openalex.org/W2085809352","https://openalex.org/W2088093305","https://openalex.org/W2088423689","https://openalex.org/W2092285329","https://openalex.org/W2092420654","https://openalex.org/W2102475066","https://openalex.org/W2103300124","https://openalex.org/W2107063279","https://openalex.org/W2108245251","https://openalex.org/W2109553965","https://openalex.org/W2112213938","https://openalex.org/W2114779636","https://openalex.org/W2128983966","https://openalex.org/W2130479394","https://openalex.org/W2131053638","https://openalex.org/W2132629607","https://openalex.org/W2133712572","https://openalex.org/W2143482176","https://openalex.org/W2148512505","https://openalex.org/W2149302140","https://openalex.org/W2160205549","https://openalex.org/W2168045053","https://openalex.org/W2169678694","https://openalex.org/W2211136176","https://openalex.org/W2274656763","https://openalex.org/W2295598076","https://openalex.org/W2318311899","https://openalex.org/W2334483166","https://openalex.org/W2336411773","https://openalex.org/W2412446857","https://openalex.org/W2440823401","https://openalex.org/W2467325716","https://openalex.org/W2471690826","https://openalex.org/W2500177451","https://openalex.org/W2583907533","https://openalex.org/W2608559058","https://openalex.org/W2625021681","https://openalex.org/W2766832305","https://openalex.org/W2774738748","https://openalex.org/W2794491987","https://openalex.org/W2886455199","https://openalex.org/W2889677957","https://openalex.org/W2893435209","https://openalex.org/W2902812092","https://openalex.org/W2905356589","https://openalex.org/W2912171584","https://openalex.org/W2921473648","https://openalex.org/W2957176022","https://openalex.org/W2970147227","https://openalex.org/W2971801381","https://openalex.org/W2972485984","https://openalex.org/W2978132989","https://openalex.org/W2979346652","https://openalex.org/W2982188446","https://openalex.org/W3004731690","https://openalex.org/W3005417975","https://openalex.org/W3007309629","https://openalex.org/W3010016408","https://openalex.org/W3015572666","https://openalex.org/W3020257619","https://openalex.org/W3023760352","https://openalex.org/W3028815767","https://openalex.org/W3035777330","https://openalex.org/W3036230820","https://openalex.org/W3043660595","https://openalex.org/W3087491618","https://openalex.org/W3092705559","https://openalex.org/W3106162654","https://openalex.org/W3120407713","https://openalex.org/W3156693194","https://openalex.org/W3157590392","https://openalex.org/W3164081635","https://openalex.org/W3172303648","https://openalex.org/W3206116522","https://openalex.org/W3215525389","https://openalex.org/W4206643900","https://openalex.org/W4211218744","https://openalex.org/W4281740412","https://openalex.org/W4289518623","https://openalex.org/W4295088922","https://openalex.org/W4308366884","https://openalex.org/W4311825396","https://openalex.org/W4322422874","https://openalex.org/W4363646126","https://openalex.org/W4380739447","https://openalex.org/W4387673203","https://openalex.org/W4389617734","https://openalex.org/W4391256965","https://openalex.org/W4394767381","https://openalex.org/W6950322510"],"related_works":["https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2093426296","https://openalex.org/W2336040088","https://openalex.org/W4402273478","https://openalex.org/W2594726310"],"abstract_inverted_index":{"Determining":[0],"the":[1,18,26,103,153],"target\u2010bound":[2],"conformation":[3,109],"of":[4,20,134,149,164],"a":[5,9,43,47,90,106],"drug\u2010like":[6],"molecule":[7,49],"is":[8],"crucial":[10],"step":[11],"in":[12,147,166],"drug":[13],"design,":[14],"as":[15,157],"it":[16],"affects":[17],"outcome":[19],"virtual":[21],"screening":[22],"(VS),":[23],"and":[24,30,131,143,177,190],"paves":[25],"way":[27],"for":[28,46,96,160,183],"hit\u2010to\u2010lead":[29],"lead":[31],"optimization.":[32],"While":[33],"most":[34],"docking":[35,132,150],"programs":[36],"usually":[37],"manage":[38],"to":[39,62,72],"produce":[40],"at":[41,196],"least":[42],"near\u2010native":[44],"pose":[45,79,97,116,156,184],"bioactive":[48],"inside":[50],"its":[51],"binding":[52],"pocket,":[53],"their":[54],"integrated":[55],"classical":[56],"scoring":[57],"functions":[58],"(SFs)":[59],"generally":[60],"fail":[61],"prioritize":[63],"this":[64,74,137],"pose.":[65],"Many":[66],"studies":[67],"have":[68],"been":[69],"carried":[70],"out":[71],"tackle":[73],"SF":[75],"problem,":[76],"offering":[77],"multiple":[78],"refinement":[80],"and/or":[81],"classification":[82],"methods,":[83],"albeit":[84],"with":[85],"limitations.":[86],"This":[87,186],"study":[88],"presents":[89],"new":[91],"support":[92],"vector":[93],"machine":[94],"model":[95,138],"classification,":[98],"called":[99],"\u201cClassyPose\u201d,":[100],"which":[101],"predicts":[102],"probability":[104],"that":[105],"receptor\u2010bound":[107],"ligand":[108,155],"could":[110],"be":[111],"near\u2010native,":[112],"without":[113],"any":[114],"additional":[115],"optimization":[117],"step.":[118],"Trained":[119],"on":[120],"protein\u2010ligand":[121],"extended":[122],"connectivity":[123],"features":[124],"extracted":[125],"from":[126],"over":[127],"21":[128],"600":[129],"crystal":[130],"poses":[133],"diverse":[135],"ligands,":[136],"outperformed":[139],"other":[140],"machine\u2010learning":[141],"algorithms":[142],"three":[144],"existing":[145],"SFs":[146],"terms":[148],"power,":[151],"identifying":[152],"native":[154],"top\u2010ranked":[158],"solution":[159],"more":[161],"than":[162],"90%":[163],"entries":[165],"two":[167],"test":[168],"sets.":[169],"It":[170],"also":[171],"achieved":[172],"high":[173],"specificity":[174],"(above":[175],"0.96),":[176],"improved":[178],"VS":[179],"performance":[180],"when":[181],"used":[182],"selection.":[185],"efficient,":[187],"user\u2010friendly":[188],"tool":[189],"all":[191],"related":[192],"data":[193],"are":[194],"available":[195],"https://github.com/vktrannguyen/Classy_Pose.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
