{"id":"https://openalex.org/W4410729131","doi":"https://doi.org/10.3389/fbinf.2025.1536504","title":"Quality over quantity: how to get the best results when using docking for repurposing","display_name":"Quality over quantity: how to get the best results when using docking for repurposing","publication_year":2025,"publication_date":"2025-05-26","ids":{"openalex":"https://openalex.org/W4410729131","doi":"https://doi.org/10.3389/fbinf.2025.1536504","pmid":"https://pubmed.ncbi.nlm.nih.gov/40491848"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1536504","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1536504","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1536504/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://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1536504/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011570640","display_name":"Lenin Dom\u00ednguez\u2010Ram\u00edrez","orcid":"https://orcid.org/0000-0002-3483-4658"},"institutions":[{"id":"https://openalex.org/I164915025","display_name":"Mexican Social Security Institute","ror":"https://ror.org/03xddgg98","country_code":"MX","type":"government","lineage":["https://openalex.org/I164915025"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Lenin Dom\u00ednguez-Ram\u00edrez","raw_affiliation_strings":["Computational Biochemistry Laboratory, Centro de Investigaci\u00f3n Biom\u00e9dica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco, Mexico"],"affiliations":[{"raw_affiliation_string":"Computational Biochemistry Laboratory, Centro de Investigaci\u00f3n Biom\u00e9dica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco, Mexico","institution_ids":["https://openalex.org/I164915025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090324795","display_name":"Maricruz Anaya-Ru\u0131\u0301z","orcid":"https://orcid.org/0000-0002-3193-3730"},"institutions":[{"id":"https://openalex.org/I164915025","display_name":"Mexican Social Security Institute","ror":"https://ror.org/03xddgg98","country_code":"MX","type":"government","lineage":["https://openalex.org/I164915025"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Maricruz Anaya-Ruiz","raw_affiliation_strings":["Cancer Cell Biology, Centro de Investigaci\u00f3n Biom\u00e9dica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco, Mexico"],"affiliations":[{"raw_affiliation_string":"Cancer Cell Biology, Centro de Investigaci\u00f3n Biom\u00e9dica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco, Mexico","institution_ids":["https://openalex.org/I164915025"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044056719","display_name":"Paulina Cort\u00e9s-Hern\u00e1ndez","orcid":"https://orcid.org/0000-0001-8226-1703"},"institutions":[{"id":"https://openalex.org/I164915025","display_name":"Mexican Social Security Institute","ror":"https://ror.org/03xddgg98","country_code":"MX","type":"government","lineage":["https://openalex.org/I164915025"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Paulina Cort\u00e9s-Hern\u00e1ndez","raw_affiliation_strings":["Computational Biochemistry Laboratory, Centro de Investigaci\u00f3n Biom\u00e9dica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco, Mexico"],"affiliations":[{"raw_affiliation_string":"Computational Biochemistry Laboratory, Centro de Investigaci\u00f3n Biom\u00e9dica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Atlixco, Mexico","institution_ids":["https://openalex.org/I164915025"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011570640","https://openalex.org/A5044056719"],"corresponding_institution_ids":["https://openalex.org/I164915025"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":4.0439,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.9379841,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"5","issue":null,"first_page":"1536504","last_page":"1536504"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9940999746322632,"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":0.9940999746322632,"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/T14351","display_name":"Statistical and Computational Modeling","score":0.9273999929428101,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.9216889142990112},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7352312207221985},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5217538475990295},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.46407178044319153},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.18009936809539795},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14850473403930664},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12928393483161926},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.06107985973358154}],"concepts":[{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.9216889142990112},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7352312207221985},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5217538475990295},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.46407178044319153},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.18009936809539795},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14850473403930664},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12928393483161926},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.06107985973358154},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1536504","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1536504","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1536504/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:40491848","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40491848","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:70b9589676b54b70979ca3652319380e","is_oa":true,"landing_page_url":"https://doaj.org/article/70b9589676b54b70979ca3652319380e","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 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12146287","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12146287","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.2025.1536504","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1536504","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1536504/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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4410729131.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1980276147","https://openalex.org/W1988437166","https://openalex.org/W2004595546","https://openalex.org/W2006617902","https://openalex.org/W2027482274","https://openalex.org/W2028629022","https://openalex.org/W2042572511","https://openalex.org/W2044444984","https://openalex.org/W2059457452","https://openalex.org/W2060341378","https://openalex.org/W2097980962","https://openalex.org/W2125801414","https://openalex.org/W2132629607","https://openalex.org/W2134967712","https://openalex.org/W2152630148","https://openalex.org/W2154558722","https://openalex.org/W2168890084","https://openalex.org/W2169678694","https://openalex.org/W2183050958","https://openalex.org/W2336040088","https://openalex.org/W2794434752","https://openalex.org/W2954297401","https://openalex.org/W3082411326","https://openalex.org/W3168430821","https://openalex.org/W3176838620","https://openalex.org/W3183900570","https://openalex.org/W3199883166","https://openalex.org/W3213672119","https://openalex.org/W4206018883","https://openalex.org/W4206912588","https://openalex.org/W4302307901","https://openalex.org/W4379769002","https://openalex.org/W4390906364","https://openalex.org/W4392093325","https://openalex.org/W4392161270"],"related_works":["https://openalex.org/W2899096130","https://openalex.org/W3190782215","https://openalex.org/W2902729297","https://openalex.org/W3110500039","https://openalex.org/W4255531208","https://openalex.org/W4396858017","https://openalex.org/W4400165188","https://openalex.org/W4206422705","https://openalex.org/W4320009247","https://openalex.org/W3186872001"],"abstract_inverted_index":{"Molecular":[0],"docking":[1,37,96,116,135,162,173],"is":[2],"among":[3],"the":[4,24,45,79,93,103,146,170],"fastest":[5],"and":[6,61,177],"most":[7],"readily":[8],"available":[9],"computational":[10],"tools":[11],"to":[12,39,51,55,159],"explore":[13],"protein-ligand":[14],"interactions.":[15],"However,":[16],"little":[17],"effort":[18],"has":[19],"been":[20],"put":[21],"into":[22],"assessing":[23],"quality":[25,94],"of":[26,95,105,152,169,180,189],"its":[27,57],"results.":[28,97],"In":[29],"this":[30,72,99],"paper,":[31],"we":[32],"compared":[33],"eight":[34],"free":[35],"license":[36],"programs":[38],"screen":[40],"a":[41,85,128,140,157,185],"drug":[42],"library":[43],"against":[44],"human":[46],"target,":[47],"phosphodiesterase":[48],"5A":[49],"(PDE5A),":[50],"evaluate":[52],"their":[53],"ability":[54],"find":[56],"known":[58,80,106],"ligand,":[59],"sildenafil,":[60],"other":[62],"ligands":[63],"that":[64,91,114,120],"became":[65,149],"erectile":[66],"dysfunction":[67],"drugs":[68],"because":[69,82],"they":[70,122],"inhibit":[71],"target.":[73],"GNINA":[74],"was":[75],"superior":[76],"at":[77],"identifying":[78],"target":[81,171],"it":[83],"offers":[84],"convolutional":[86],"neural":[87],"network":[88],"(CNN)":[89],"score":[90,101,130,187],"ranks":[92],"Using":[98],"CNN":[100,129,186],"improved":[102],"ranking":[104,133],"positives.":[107],"Receiver":[108],"operating":[109],"characteristic":[110],"(ROC)":[111],"analysis":[112],"revealed":[113],"all":[115],"suites":[117],"lack":[118],"specificity;":[119],"is,":[121],"often":[123],"misidentify":[124],"true":[125],"negatives.":[126],"Employing":[127],"cutoff":[131,188],"before":[132],"by":[134],"affinity":[136],"raised":[137],"specificity":[138],"with":[139],"small":[141],"loss":[142],"in":[143],"sensitivity.":[144],"After":[145],"cutoff,":[147],"datasets":[148],"smaller":[150],"but":[151],"higher":[153],"quality.":[154],"We":[155],"propose":[156],"heuristic":[158],"produce":[160],"relevant":[161],"results,":[163],"which":[164],"includes":[165],"an":[166,178],"overall":[167],"evaluation":[168],"on":[172],"performance":[174],"through":[175],"ROC":[176],"improvement":[179],"candidate":[181],"binder":[182],"selection":[183],"using":[184],"0.9.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
