{"id":"https://openalex.org/W2119512897","doi":"https://doi.org/10.1186/1758-2946-5-26","title":"Open-source platform to benchmark fingerprints for ligand-based virtual screening","display_name":"Open-source platform to benchmark fingerprints for ligand-based virtual screening","publication_year":2013,"publication_date":"2013-05-30","ids":{"openalex":"https://openalex.org/W2119512897","doi":"https://doi.org/10.1186/1758-2946-5-26","mag":"2119512897","pmid":"https://pubmed.ncbi.nlm.nih.gov/23721588"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-26","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-26","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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-26","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019754904","display_name":"Sereina Riniker","orcid":"https://orcid.org/0000-0003-1893-4031"},"institutions":[{"id":"https://openalex.org/I4400600974","display_name":"Novartis Institutes for BioMedical Research","ror":"https://ror.org/053gv2m95","country_code":null,"type":"funder","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]},{"id":"https://openalex.org/I1283582996","display_name":"Novartis (Switzerland)","ror":"https://ror.org/02f9zrr09","country_code":"CH","type":"company","lineage":["https://openalex.org/I1283582996"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Sereina Riniker","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Basel, Switzerland. gregory.landrum@novartis.com","Novartis Institutes for Biomedical Research, Basel,  Switzerland"],"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Basel, Switzerland. gregory.landrum@novartis.com","institution_ids":[]},{"raw_affiliation_string":"Novartis Institutes for Biomedical Research, Basel,  Switzerland","institution_ids":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056808182","display_name":"Gregory A. Landrum","orcid":"https://orcid.org/0000-0001-6279-4481"},"institutions":[{"id":"https://openalex.org/I1283582996","display_name":"Novartis (Switzerland)","ror":"https://ror.org/02f9zrr09","country_code":"CH","type":"company","lineage":["https://openalex.org/I1283582996"]},{"id":"https://openalex.org/I4400600974","display_name":"Novartis Institutes for BioMedical Research","ror":"https://ror.org/053gv2m95","country_code":null,"type":"funder","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gregory A Landrum","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Basel, Switzerland","Novartis Institutes for Biomedical Research, Basel,  Switzerland"],"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Basel, Switzerland","institution_ids":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]},{"raw_affiliation_string":"Novartis Institutes for Biomedical Research, Basel,  Switzerland","institution_ids":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5019754904"],"corresponding_institution_ids":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":18.4934,"has_fulltext":true,"cited_by_count":387,"citation_normalized_percentile":{"value":0.99550761,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"5","issue":"1","first_page":"26","last_page":"26"},"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":0.9751999974250793,"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/T12255","display_name":"Biosimilars and Bioanalytical Methods","score":0.9696999788284302,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8282690048217773},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8280490636825562},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6883673667907715},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6295573115348816},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5897378325462341},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.569401204586029},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.511083722114563},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4635801315307617},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4010535478591919},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2411794662475586},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.16866734623908997},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.122565358877182},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.07726472616195679}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8282690048217773},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8280490636825562},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6883673667907715},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6295573115348816},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5897378325462341},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.569401204586029},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.511083722114563},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4635801315307617},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4010535478591919},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2411794662475586},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.16866734623908997},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.122565358877182},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.07726472616195679},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1758-2946-5-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-26","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-26","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:23721588","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23721588","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:2685555","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3686626","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"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/88800","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/88800","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Journal of Cheminformatics, 5","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000088800","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000088800","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-5-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-26","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-26","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/F4320333796","display_name":"Novartis Institutes for BioMedical Research","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119512897.pdf","grobid_xml":"https://content.openalex.org/works/W2119512897.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1487942432","https://openalex.org/W1545231783","https://openalex.org/W1964513093","https://openalex.org/W1965138864","https://openalex.org/W1974758710","https://openalex.org/W1974880836","https://openalex.org/W1977934535","https://openalex.org/W1983332050","https://openalex.org/W1988037271","https://openalex.org/W1988909822","https://openalex.org/W1991262449","https://openalex.org/W1996973304","https://openalex.org/W2000541041","https://openalex.org/W2001816314","https://openalex.org/W2003752196","https://openalex.org/W2005465759","https://openalex.org/W2008732224","https://openalex.org/W2013090273","https://openalex.org/W2015907087","https://openalex.org/W2016979469","https://openalex.org/W2017547569","https://openalex.org/W2020118174","https://openalex.org/W2021574925","https://openalex.org/W2021723901","https://openalex.org/W2021748110","https://openalex.org/W2024610405","https://openalex.org/W2025135899","https://openalex.org/W2038310963","https://openalex.org/W2038361288","https://openalex.org/W2042110087","https://openalex.org/W2052826484","https://openalex.org/W2060531713","https://openalex.org/W2061237926","https://openalex.org/W2064440950","https://openalex.org/W2064576005","https://openalex.org/W2075769043","https://openalex.org/W2081266727","https://openalex.org/W2096541451","https://openalex.org/W2100916935","https://openalex.org/W2112912103","https://openalex.org/W2125253492","https://openalex.org/W2125792789","https://openalex.org/W2176516200","https://openalex.org/W2320034101","https://openalex.org/W2330150548","https://openalex.org/W2582743722","https://openalex.org/W4241727697","https://openalex.org/W4253863064"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W4302604134","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W4211197663","https://openalex.org/W2491403535","https://openalex.org/W3123068371","https://openalex.org/W2479811461","https://openalex.org/W2104915799","https://openalex.org/W2355429491"],"abstract_inverted_index":{":":[0],"Similarity-search":[1],"methods":[2,55,157,217],"using":[3,29],"molecular":[4],"fingerprints":[5,18,146,152,173,185],"are":[6,158,218],"an":[7],"important":[8],"tool":[9],"for":[10,83,98,123,138,143],"ligand-based":[11],"virtual":[12],"screening.":[13],"A":[14],"huge":[15],"variety":[16],"of":[17,70,86,110,115,127,136,203,215],"exist":[19],"and":[20,35,48,74,101,113,134,174],"their":[21,211],"performance,":[22],"usually":[23],"assessed":[24,153],"in":[25,59,191],"retrospective":[26],"benchmarking":[27,85],"studies":[28],"data":[30,45,72,97,111],"sets":[31,46,73],"with":[32,148,161],"known":[33,36],"actives":[34,100],"or":[37],"assumed":[38],"inactives,":[39],"depends":[40],"largely":[41],"on":[42],"the":[43,49,68,84,99,131,162,171,182,189,204],"validation":[44],"used":[47,103,122],"similarity":[50],"measure":[51],"used.":[52],"Comparing":[53],"new":[54],"to":[56,67,120,220],"existing":[57],"ones":[58],"any":[60],"systematic":[61],"way":[62],"is":[63],"rather":[64],"difficult":[65],"due":[66],"lack":[69],"standard":[71,81,145],"evaluation":[75,156,206],"procedures.":[76],"Here,":[77],"we":[78],"present":[79],"a":[80,175,192],"platform":[82,91],"2D":[87],"fingerprints.":[88],"The":[89,141],"open-source":[90],"contains":[92],"all":[93],"source":[94],"code,":[95],"structural":[96],"inactives":[102],"(drawn":[104],"from":[105,188],"three":[106],"publicly":[107],"available":[108],"collections":[109],"sets),":[112],"lists":[114],"randomly":[116],"selected":[117],"query":[118],"molecules":[119],"be":[121],"statistically":[124,193],"valid":[125],"comparisons":[126],"methods.":[128,165],"This":[129],"allows":[130],"exact":[132],"reproduction":[133],"comparison":[135],"results":[137,142],"future":[139],"studies.":[140],"12":[144,172],"together":[147,160],"two":[149,183],"simple":[150],"baseline":[151,184],"by":[154],"seven":[155,205],"shown":[159],"correlations":[163,167,197],"between":[164,170,201],"High":[166,196],"were":[168,186,198],"found":[169,200],"careful":[176],"statistical":[177],"analysis":[178],"showed":[179],"that":[180,209],"only":[181],"different":[187],"others":[190],"significant":[194],"way.":[195],"also":[199],"six":[202],"methods,":[207],"indicating":[208],"despite":[210],"seeming":[212],"differences,":[213],"many":[214],"these":[216],"similar":[219],"each":[221],"other.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":55},{"year":2023,"cited_by_count":28},{"year":2022,"cited_by_count":36},{"year":2021,"cited_by_count":57},{"year":2020,"cited_by_count":60},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":22},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}
