{"id":"https://openalex.org/W7131794370","doi":"https://doi.org/10.3389/fbinf.2026.1756279","title":"An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation","display_name":"An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation","publication_year":2026,"publication_date":"2026-02-27","ids":{"openalex":"https://openalex.org/W7131794370","doi":"https://doi.org/10.3389/fbinf.2026.1756279","pmid":"https://pubmed.ncbi.nlm.nih.gov/41836753"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2026.1756279","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2026.1756279","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1756279/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1756279/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075289984","display_name":"Stefan Ivanov","orcid":"https://orcid.org/0000-0002-6949-2328"},"institutions":[{"id":"https://openalex.org/I24768866","display_name":"Bulgarian Academy of Sciences","ror":"https://ror.org/01x8hew03","country_code":"BG","type":"government","lineage":["https://openalex.org/I24768866"]},{"id":"https://openalex.org/I30147112","display_name":"Medical University of Sofia","ror":"https://ror.org/01n9zy652","country_code":"BG","type":"education","lineage":["https://openalex.org/I30147112"]},{"id":"https://openalex.org/I4210103918","display_name":"Institute of Biophysics and Biomedical Engineering","ror":"https://ror.org/01dxqkr82","country_code":"BG","type":"facility","lineage":["https://openalex.org/I24768866","https://openalex.org/I4210103918"]},{"id":"https://openalex.org/I4210141563","display_name":"Institute of Information Technologies","ror":"https://ror.org/03ypsgm65","country_code":"BG","type":"facility","lineage":["https://openalex.org/I24768866","https://openalex.org/I4210141563"]}],"countries":["BG"],"is_corresponding":true,"raw_author_name":"Stefan M. Ivanov","raw_affiliation_strings":["Centre of Excellence in Informatics and Information and Communication Technologies","Faculty of Pharmacy, Medical University of Sofia","Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences"],"affiliations":[{"raw_affiliation_string":"Centre of Excellence in Informatics and Information and Communication Technologies","institution_ids":["https://openalex.org/I4210141563"]},{"raw_affiliation_string":"Faculty of Pharmacy, Medical University of Sofia","institution_ids":["https://openalex.org/I30147112"]},{"raw_affiliation_string":"Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences","institution_ids":["https://openalex.org/I4210103918","https://openalex.org/I24768866"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5075289984"],"corresponding_institution_ids":["https://openalex.org/I24768866","https://openalex.org/I30147112","https://openalex.org/I4210103918","https://openalex.org/I4210141563"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.47296786,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":null,"first_page":"1756279","last_page":"1756279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9757000207901001,"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":0.9757000207901001,"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":0.006099999882280827,"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/T13180","display_name":"Chemistry and Chemical Engineering","score":0.001500000013038516,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7174999713897705},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5619000196456909},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5188999772071838},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5087000131607056},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47440001368522644},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4643999934196472},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4471000134944916},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.3930000066757202}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7174999713897705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6782000064849854},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5619000196456909},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.558899998664856},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5188999772071838},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5087000131607056},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47440001368522644},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4643999934196472},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4471000134944916},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.3930000066757202},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35370001196861267},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.3375999927520752},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.32989999651908875},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.3163999915122986},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.2874000072479248},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.2847000062465668},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28029999136924744},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.27619999647140503},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2637999951839447},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.26089999079704285},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.258899986743927}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2026.1756279","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2026.1756279","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1756279/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41836753","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41836753","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:e533754bc3214afc9b2bbbb6cde4de5e","is_oa":true,"landing_page_url":"https://doaj.org/article/e533754bc3214afc9b2bbbb6cde4de5e","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":"Frontiers in Bioinformatics, Vol 6 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12982188","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12982188/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2026.1756279","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2026.1756279","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1756279/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5391346216201782,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1563449336","display_name":null,"funder_award_id":"BG-RRP-2.004-0004-C01","funder_id":"https://openalex.org/F7311471023","funder_display_name":"NextGenerationEU"}],"funders":[{"id":"https://openalex.org/F7311471023","display_name":"NextGenerationEU","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7131794370.pdf"},"referenced_works_count":148,"referenced_works":["https://openalex.org/W1605886981","https://openalex.org/W1827840064","https://openalex.org/W1954736746","https://openalex.org/W1964513093","https://openalex.org/W1967052111","https://openalex.org/W1968319881","https://openalex.org/W1969189143","https://openalex.org/W1976149536","https://openalex.org/W1976499671","https://openalex.org/W1981167315","https://openalex.org/W1981225934","https://openalex.org/W1988385430","https://openalex.org/W2004386051","https://openalex.org/W2008535813","https://openalex.org/W2013551774","https://openalex.org/W2014276094","https://openalex.org/W2029087609","https://openalex.org/W2030980866","https://openalex.org/W2031390939","https://openalex.org/W2034012751","https://openalex.org/W2035266068","https://openalex.org/W2042382355","https://openalex.org/W2043509228","https://openalex.org/W2058433776","https://openalex.org/W2058820833","https://openalex.org/W2061583504","https://openalex.org/W2066690664","https://openalex.org/W2067174909","https://openalex.org/W2071969518","https://openalex.org/W2071979436","https://openalex.org/W2078374001","https://openalex.org/W2086815823","https://openalex.org/W2087925988","https://openalex.org/W2092285329","https://openalex.org/W2093221728","https://openalex.org/W2095719702","https://openalex.org/W2096914244","https://openalex.org/W2118233996","https://openalex.org/W2124879768","https://openalex.org/W2127760066","https://openalex.org/W2137170709","https://openalex.org/W2147993766","https://openalex.org/W2154139219","https://openalex.org/W2159367911","https://openalex.org/W2164656750","https://openalex.org/W2169678694","https://openalex.org/W2214665483","https://openalex.org/W2332764255","https://openalex.org/W2404280981","https://openalex.org/W2510867035","https://openalex.org/W2517337142","https://openalex.org/W2522743012","https://openalex.org/W2526925775","https://openalex.org/W2533899942","https://openalex.org/W2535433376","https://openalex.org/W2535482197","https://openalex.org/W2536259549","https://openalex.org/W2549923062","https://openalex.org/W2560915683","https://openalex.org/W2569644332","https://openalex.org/W2618054076","https://openalex.org/W2743262308","https://openalex.org/W2743999803","https://openalex.org/W2784213390","https://openalex.org/W2786243118","https://openalex.org/W2794598909","https://openalex.org/W2794694420","https://openalex.org/W2803094965","https://openalex.org/W2808089837","https://openalex.org/W2825109425","https://openalex.org/W2905720145","https://openalex.org/W2916534270","https://openalex.org/W2981386748","https://openalex.org/W2989052455","https://openalex.org/W3015572666","https://openalex.org/W3019541266","https://openalex.org/W3030948478","https://openalex.org/W3034934060","https://openalex.org/W3036788014","https://openalex.org/W3040072668","https://openalex.org/W3045367216","https://openalex.org/W3087004338","https://openalex.org/W3088316485","https://openalex.org/W3093615621","https://openalex.org/W3093856364","https://openalex.org/W3094686696","https://openalex.org/W3118488899","https://openalex.org/W3126031592","https://openalex.org/W3128646645","https://openalex.org/W3131728774","https://openalex.org/W3132756803","https://openalex.org/W3149078497","https://openalex.org/W3160229201","https://openalex.org/W3162274578","https://openalex.org/W3164542691","https://openalex.org/W3168430821","https://openalex.org/W3187980261","https://openalex.org/W3198869316","https://openalex.org/W3212543990","https://openalex.org/W4205632467","https://openalex.org/W4206509885","https://openalex.org/W4214530112","https://openalex.org/W4245700002","https://openalex.org/W4280575759","https://openalex.org/W4281776684","https://openalex.org/W4282006454","https://openalex.org/W4283835519","https://openalex.org/W4285010958","https://openalex.org/W4294955967","https://openalex.org/W4297914802","https://openalex.org/W4313339550","https://openalex.org/W4315433138","https://openalex.org/W4319164354","https://openalex.org/W4323807713","https://openalex.org/W4361301986","https://openalex.org/W4367179611","https://openalex.org/W4376642820","https://openalex.org/W4379599683","https://openalex.org/W4385341201","https://openalex.org/W4387639561","https://openalex.org/W4388429679","https://openalex.org/W4388928772","https://openalex.org/W4389157189","https://openalex.org/W4390114224","https://openalex.org/W4392716328","https://openalex.org/W4392748256","https://openalex.org/W4393931011","https://openalex.org/W4394688967","https://openalex.org/W4394729858","https://openalex.org/W4394935805","https://openalex.org/W4396891056","https://openalex.org/W4399416193","https://openalex.org/W4400007971","https://openalex.org/W4400112692","https://openalex.org/W4400120249","https://openalex.org/W4400245753","https://openalex.org/W4400284461","https://openalex.org/W4401212569","https://openalex.org/W4402040352","https://openalex.org/W4402403664","https://openalex.org/W4402626987","https://openalex.org/W4405249417","https://openalex.org/W4406193027","https://openalex.org/W4407875892","https://openalex.org/W4411493044","https://openalex.org/W4412417845","https://openalex.org/W4412629505","https://openalex.org/W7124282062"],"related_works":[],"abstract_inverted_index":{"Modern":[0],"virtual":[1],"high-throughput":[2],"screening":[3],"(VHTS)":[4],"pipelines":[5,209],"can":[6,102,129,233],"be":[7,103,130,161],"suboptimally":[8],"validated,":[9],"with":[10],"no":[11,88],"rigorous":[12],"studies":[13,36,187],"conclusively":[14],"demonstrating":[15],"that":[16,68,86,101,210,220],"every":[17,170],"one":[18],"of":[19,45,98,120,126,134,176,180,195,242],"their":[20],"steps":[21],"reliably":[22],"adds":[23],"increasing":[24],"enrichment":[25],"atop":[26],"the":[27,42,46,52,56,174,193,237,243],"baseline":[28],"random":[29],"hit":[30,213],"rate.":[31],"Moreover,":[32],"what":[33],"little":[34],"benchmarking":[35],"are":[37,147,156,159],"available":[38],"primarily":[39],"focus":[40],"on":[41],"docking":[43],"aspect":[44],"pipelines,":[47],"which":[48],"is":[49,203],"usually":[50],"only":[51],"beginning":[53],"or":[54,199],"near":[55],"beginning,":[57],"and":[58,82,92,116,136,146,183,190,208,215,231],"even":[59],"there,":[60],"authors":[61],"tend":[62],"to":[63,79,150,160,188,204,222,235],"use":[64],"flawed":[65],"data":[66,83,100,128,138,179],"sets":[67,133,155],"artificially":[69],"inflate":[70],"performance":[71,168],"metrics.":[72],"Herein,":[73],"we":[74],"present":[75],"an":[76],"alternative":[77],"method":[78],"pipeline":[80,107,151],"validation":[81,186],"set":[84],"generation":[85],"requires":[87],"additional":[89],"experimental":[90,114],"work":[91],"expenditure,":[93],"yet":[94],"offers":[95],"vast":[96],"amounts":[97,125],"negative":[99,127,137,178],"used":[104],"in":[105,142,185],"VHTS":[106],"validation.":[108,152],"By":[109],"randomizing":[110],"ligands":[111],"across":[112],"published":[113],"structures":[115],"generating":[117],"structural":[118],"isomers":[119],"known":[121],"binders,":[122],"practically":[123],"unlimited":[124],"generated.":[131],"Such":[132],"positive":[135],"points":[139],"match":[140],"closely":[141],"key":[143],"molecular":[144],"properties":[145],"well":[148],"suited":[149],"Once":[153],"such":[154],"generated,":[157],"they":[158],"run":[162],"through":[163],"any":[164],"proposed":[165],"pipeline,":[166],"assessing":[167],"at":[169],"step.":[171],"We":[172],"stress":[173],"importance":[175],"using":[177],"adequate":[181],"quality":[182],"quantity":[184],"definitively":[189],"verifiably":[191],"demonstrate":[192],"utility":[194],"a":[196],"given":[197],"tool":[198],"workflow.":[200],"Our":[201],"goal":[202],"help":[205],"distinguish":[206],"tools":[207],"truly":[211],"accelerate":[212],"discovery":[214],"lead":[216],"optimization":[217],"from":[218],"ones":[219],"promise":[221],"do":[223,227],"so":[224],"but":[225],"actually":[226],"not,":[228],"whereupon":[229],"academia":[230],"industry":[232],"begin":[234],"tackle":[236],"many":[238],"unaddressed":[239],"medical":[240],"needs":[241],"21st":[244],"century.":[245]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-02-27T00:00:00"}