{"id":"https://openalex.org/W2162960404","doi":"https://doi.org/10.1186/1758-2946-5-50","title":"Improving structural similarity based virtual screening using background knowledge","display_name":"Improving structural similarity based virtual screening using background knowledge","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2162960404","doi":"https://doi.org/10.1186/1758-2946-5-50","mag":"2162960404","pmid":"https://pubmed.ncbi.nlm.nih.gov/24341870"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-50","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-50","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-50","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-50","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030634901","display_name":"Tobias Girschick","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Girschick","raw_affiliation_strings":["Technische Universit\u00e4t M\u00fcnchen, Institut f\u00fcr Informatik, Boltzmannstrasse 3, 85748, Garching b. M\u00fcnchen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technische Universit\u00e4t M\u00fcnchen, Institut f\u00fcr Informatik, Boltzmannstrasse 3, 85748, Garching b. M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039284866","display_name":"Lucia Puchbauer","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lucia Puchbauer","raw_affiliation_strings":["Technische Universit\u00e4t M\u00fcnchen, Institut f\u00fcr Informatik, Boltzmannstrasse 3, 85748, Garching b. M\u00fcnchen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Technische Universit\u00e4t M\u00fcnchen, Institut f\u00fcr Informatik, Boltzmannstrasse 3, 85748, Garching b. M\u00fcnchen, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006247481","display_name":"Stefan Kr\u00e4mer","orcid":"https://orcid.org/0000-0002-0071-9344"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Stefan Kramer","raw_affiliation_strings":["Johannes Gutenberg-Universit\u00e4t Mainz, Institut f\u00fcr Informatik, Staudingerweg 9, 55128 Mainz, Germany. kramer@informatik.uni-mainz.de","Johannes Gutenberg-Universit\u00e4t Mainz, Institut f\u00fcr Informatik, Staudingerweg 9, 55128, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johannes Gutenberg-Universit\u00e4t Mainz, Institut f\u00fcr Informatik, Staudingerweg 9, 55128 Mainz, Germany. kramer@informatik.uni-mainz.de","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Johannes Gutenberg-Universit\u00e4t Mainz, Institut f\u00fcr Informatik, Staudingerweg 9, 55128, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006247481"],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1099,"currency":"EUR","value_usd":1185},"fwci":1.0936,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.80222041,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"5","issue":"1","first_page":"50","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.984499990940094,"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":0.984499990940094,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.0017000000225380063,"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":0.7585834264755249},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.7360681295394897},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.700615406036377},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6966103315353394},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6616111993789673},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.5323458313941956},{"id":"https://openalex.org/keywords/similarity-measure","display_name":"Similarity measure","score":0.5176392197608948},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.514474630355835},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4675176441669464},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.46741724014282227},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.4568342864513397},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.43628332018852234},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.43531420826911926},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3118264079093933},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21828928589820862},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14442428946495056},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.11997130513191223}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7585834264755249},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.7360681295394897},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.700615406036377},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6966103315353394},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6616111993789673},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.5323458313941956},{"id":"https://openalex.org/C2776517306","wikidata":"https://www.wikidata.org/wiki/Q29017317","display_name":"Similarity measure","level":2,"score":0.5176392197608948},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.514474630355835},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4675176441669464},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.46741724014282227},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.4568342864513397},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43628332018852234},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.43531420826911926},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3118264079093933},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21828928589820862},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14442428946495056},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.11997130513191223},{"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/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-5-50","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-50","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-50","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":"pmid:24341870","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24341870","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 cheminformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2927954","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3928642","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:10.1186/1758-2946-5-50","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-50","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-50","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":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162960404.pdf","grobid_xml":"https://content.openalex.org/works/W2162960404.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W1607804102","https://openalex.org/W1977644047","https://openalex.org/W1988037271","https://openalex.org/W1988564488","https://openalex.org/W2021574925","https://openalex.org/W2027378911","https://openalex.org/W2027482274","https://openalex.org/W2038702914","https://openalex.org/W2046509566","https://openalex.org/W2060531713","https://openalex.org/W2066528812","https://openalex.org/W2077440882","https://openalex.org/W2096725584","https://openalex.org/W2107841008","https://openalex.org/W2112912103","https://openalex.org/W2116513829","https://openalex.org/W2127760066","https://openalex.org/W2130479394","https://openalex.org/W2137052779","https://openalex.org/W2142553313","https://openalex.org/W2144903778","https://openalex.org/W2146211839","https://openalex.org/W3175318380"],"related_works":["https://openalex.org/W3180887190","https://openalex.org/W2320211095","https://openalex.org/W2308164565","https://openalex.org/W2062768126","https://openalex.org/W3003855012","https://openalex.org/W2347569454","https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2594726310","https://openalex.org/W2355193834"],"abstract_inverted_index":{"BACKGROUND:":[0],"Virtual":[1],"screening":[2,59,110,180],"in":[3,12,45,86,138,178,205],"the":[4,13,77,80,87,128,131,139,147,150,196],"form":[5,88,140],"of":[6,67,79,89,125,130,141,149,195],"similarity":[7,27,34,74,81,133,151,176],"rankings":[8,177],"is":[9,202,215,224],"often":[10],"applied":[11,123,233],"early":[14],"drug":[15,206],"discovery":[16,207],"process":[17],"to":[18,42,173,190,234],"rank":[19],"and":[20,60,181,208,226],"prioritize":[21],"compounds":[22],"from":[23],"a":[24,54,72,142],"database.":[25],"This":[26,83,201],"ranking":[28],"can":[29,40,93,171,188,231],"be":[30,95,232],"achieved":[31],"with":[32,121,135,153,157],"structural":[33,73,132],"measures.":[35],"However,":[36],"their":[37],"general":[38],"nature":[39],"lead":[41,172,189],"insufficient":[43],"performance":[44],"some":[46],"application":[47],"cases.":[48],"In":[49,108],"this":[50],"paper,":[51],"we":[52,112],"provide":[53],"link":[55],"between":[56],"ranking-based":[57],"virtual":[58,109,179],"fragment-based":[61,103],"data":[62,104,158,185],"mining":[63,105,159,186],"methods.":[64,106,160],"The":[65],"inclusion":[66],"binding-relevant":[68],"background":[69,84,136,154,169,197],"knowledge":[70,85,137,155,170,198],"into":[71],"measure":[75,134,152],"improves":[76,118],"quality":[78],"rankings.":[82],"binding":[90,167,222],"relevant":[91,144,168],"substructures":[92],"either":[94],"derived":[96,156],"by":[97,101],"hand":[98],"selection":[99],"or":[100,146,217],"automated":[102],"RESULTS:":[107],"experiments":[111],"show":[113],"that":[114,165,182],"our":[115,126],"approach":[116],"clearly":[117],"enrichment":[119],"factors":[120],"both":[122],"variants":[124],"approach:":[127],"extension":[129,148],"hand-selected":[143],"substructure":[145],"CONCLUSION:":[161],"Our":[162],"study":[163],"shows":[164],"adding":[166],"significantly":[174],"improved":[175],"even":[183],"basic":[184],"approaches":[187,230],"competitive":[191],"results":[192],"making":[193],"hand-selection":[194],"less":[199],"crucial.":[200],"especially":[203],"important":[204],"development":[209],"projects":[210],"where":[211],"no":[212,220],"receptor":[213],"structure":[214],"available":[216],"more":[218],"frequently":[219],"verified":[221],"mode":[223],"known":[225],"mostly":[227],"ligand":[228],"based":[229],"generate":[235],"hit":[236],"compounds.":[237]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}