{"id":"https://openalex.org/W2007026358","doi":"https://doi.org/10.1186/1758-2946-3-s1-p41","title":"Evaluation of different machine learning methods for ligand-based virtual screening","display_name":"Evaluation of different machine learning methods for ligand-based virtual screening","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2007026358","doi":"https://doi.org/10.1186/1758-2946-3-s1-p41","mag":"2007026358"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-p41","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p41","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-P41","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-P41","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060640473","display_name":"Rafa\u0142 Kurczab","orcid":"https://orcid.org/0000-0002-9555-3905"},"institutions":[{"id":"https://openalex.org/I4210120768","display_name":"Maj Institute of Pharmacology","ror":"https://ror.org/0288swk05","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"funder","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"R Kurczab","raw_affiliation_strings":["Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-343, Poland","Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Krak\u00f3w, Poland"],"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-343, Poland","institution_ids":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]},{"raw_affiliation_string":"Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Krak\u00f3w, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108421908","display_name":"Sabina Smusz","orcid":null},"institutions":[{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"funder","lineage":["https://openalex.org/I99542240"]},{"id":"https://openalex.org/I4210120768","display_name":"Maj Institute of Pharmacology","ror":"https://ror.org/0288swk05","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"S Smusz","raw_affiliation_strings":["Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-343, Poland","Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Krak\u00f3w, Poland"],"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-343, Poland","institution_ids":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]},{"raw_affiliation_string":"Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Krak\u00f3w, Poland","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025399512","display_name":"Andrzej J. Bojarski","orcid":"https://orcid.org/0000-0003-1417-6333"},"institutions":[{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"funder","lineage":["https://openalex.org/I99542240"]},{"id":"https://openalex.org/I4210120768","display_name":"Maj Institute of Pharmacology","ror":"https://ror.org/0288swk05","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"AJ Bojarski","raw_affiliation_strings":["Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-343, Poland","Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Krak\u00f3w, Poland"],"affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-343, Poland","institution_ids":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]},{"raw_affiliation_string":"Department of Medicinal Chemistry Institute of Pharmacology, Polish Academy of Sciences, Krak\u00f3w, Poland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060640473"],"corresponding_institution_ids":["https://openalex.org/I4210120768","https://openalex.org/I99542240"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.09294872,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"3","issue":"S1","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":0.9997000098228455,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9678999781608582,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.909600019454956,"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":0.8186020255088806},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7101401090621948},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40717756748199463},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36601150035858154},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3600187301635742},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3512119650840759},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.2649305462837219},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19215193390846252},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07151982188224792}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8186020255088806},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7101401090621948},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40717756748199463},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36601150035858154},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3600187301635742},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3512119650840759},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2649305462837219},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19215193390846252},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07151982188224792}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-p41","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p41","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-P41","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:7a5100b7f34a48238d6f7c8c19ee5089","is_oa":true,"landing_page_url":"https://doaj.org/article/7a5100b7f34a48238d6f7c8c19ee5089","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 3, Iss Suppl 1, p P41 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091978","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083598","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-s1-p41","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p41","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-3-S1-P41","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320335197","display_name":"Norway Grants","ror":"https://ror.org/02dfxg175"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2007026358.pdf","grobid_xml":"https://content.openalex.org/works/W2007026358.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2105029490","https://openalex.org/W2121776789","https://openalex.org/W2133990480","https://openalex.org/W2157914995"],"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/W4313488044","https://openalex.org/W3209574120","https://openalex.org/W4312192474","https://openalex.org/W4210805261"],"abstract_inverted_index":{"In":[0,32],"silico":[1],"High":[2],"Throughput":[3],"Screening":[4],"of":[5,14,24,38,96,111,119,122,126,136,141,146,176],"large":[6],"compound":[7],"databases":[8],"has":[9,150],"become":[10],"increasingly":[11],"popular":[12],"technology":[13],"finding":[15],"valuable":[16],"drug":[17],"candidates,":[18],"by":[19],"applying":[20],"a":[21,94],"wide":[22],"range":[23],"computational":[25],"methods,":[26,65],"such":[27,66],"as":[28],"machine":[29,40,63,97,165],"learning":[30,41,64,98,166],"[1].":[31],"recent":[33],"years,":[34],"many":[35,87],"comparative":[36],"studies":[37],"different":[39,62,120],"methods":[42,132],"performance":[43],"in":[44,104],"ligand-based":[45],"virtual":[46],"screening":[47],"have":[48,58,115],"been":[49,151],"reported":[50],"[2,3].\r\n\r\nIn":[51],"order":[52],"to":[53,153],"extend":[54],"these":[55],"studies,":[56],"we":[57,114],"evaluated":[59],"over":[60],"60":[61],"as:":[67],"support":[68],"vector":[69],"machines":[70],"(with":[71],"and":[72,86,129,139,156,181],"without":[73],"parameter":[74],"optimization),":[75],"naive":[76],"Bayesian,":[77],"decision":[78],"trees,":[79],"random":[80],"forest,":[81],"meta-classifiers":[82],"(boosting,":[83],"bagging,":[84],"grading)":[85],"others.":[88],"All":[89],"calculations":[90],"were":[91],"performed":[92],"using":[93],"collection":[95],"algorithms":[99],"for":[100,109],"data":[101],"mining":[102],"implemented":[103],"WEKA":[105],"package":[106],"[4].":[107],"Additionally,":[108],"each":[110],"the":[112,117,124,134,171],"method,":[113],"examined":[116],"influence":[118],"type":[121],"fingerprints,":[123],"size":[125],"training":[127,155],"sets":[128],"attribute":[130],"selection":[131],"on":[133],"rate":[135],"active":[137],"recall":[138],"precision":[140],"selection.":[142],"Our":[143],"internal":[144],"database":[145],"known":[147],"5-HT7":[148],"antagonists":[149],"used":[152],"build":[154],"testing":[157],"sets.\r\n\r\nIt":[158],"was":[159],"found":[160],"that":[161,168],"there":[162],"is":[163],"no":[164],"approach":[167],"consistently":[169],"provides":[170],"best":[172],"results":[173],"but":[174],"some":[175],"them":[177],"are":[178],"very":[179],"stable":[180],"can":[182],"be":[183],"applied":[184],"universally.":[185]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}
