{"id":"https://openalex.org/W4416060094","doi":"https://doi.org/10.1093/bioinformatics/btaf604","title":"Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms","display_name":"Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4416060094","doi":"https://doi.org/10.1093/bioinformatics/btaf604","pmid":"https://pubmed.ncbi.nlm.nih.gov/41206130"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf604","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf604","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf604","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072690705","display_name":"Melissa Van Norden","orcid":"https://orcid.org/0000-0002-6190-7381"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Melissa Van Norden","raw_affiliation_strings":["Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071956904","display_name":"William Mangione","orcid":"https://orcid.org/0000-0003-0582-4247"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Mangione","raw_affiliation_strings":["Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062735324","display_name":"Zackary Falls","orcid":"https://orcid.org/0000-0003-4116-0441"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zackary Falls","raw_affiliation_strings":["Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059358345","display_name":"Ram Samudrala","orcid":"https://orcid.org/0000-0001-9069-8497"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ram Samudrala","raw_affiliation_strings":["Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, NY 14203, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5072690705"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3510529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"11","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":0.8748999834060669,"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":0.8748999834060669,"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":0.023600000888109207,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.00419999985024333,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8560000061988831},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4271000027656555},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4004000127315521},{"id":"https://openalex.org/keywords/drug-industry","display_name":"Drug industry","score":0.29980000853538513},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.26980000734329224}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8560000061988831},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7146000266075134},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4715000092983246},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4271000027656555},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4004000127315521},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3312000036239624},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.32519999146461487},{"id":"https://openalex.org/C2993777677","wikidata":"https://www.wikidata.org/wiki/Q507443","display_name":"Drug industry","level":2,"score":0.29980000853538513},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.27880001068115234},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2766999900341034},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.26980000734329224},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2615000009536743},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2563000023365021},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.25130000710487366}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf604","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf604","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41206130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41206130","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11418501","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12607264","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:10.1093/bioinformatics/btaf604","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf604","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":137,"referenced_works":["https://openalex.org/W1531262373","https://openalex.org/W1975681040","https://openalex.org/W1977282213","https://openalex.org/W1985761301","https://openalex.org/W1987134040","https://openalex.org/W1994658365","https://openalex.org/W1998898494","https://openalex.org/W2017285544","https://openalex.org/W2031954078","https://openalex.org/W2032909496","https://openalex.org/W2039936465","https://openalex.org/W2047293109","https://openalex.org/W2049263517","https://openalex.org/W2049716588","https://openalex.org/W2050078980","https://openalex.org/W2061016350","https://openalex.org/W2107118079","https://openalex.org/W2113072832","https://openalex.org/W2130479394","https://openalex.org/W2132094707","https://openalex.org/W2134881479","https://openalex.org/W2140538197","https://openalex.org/W2155201844","https://openalex.org/W2166550586","https://openalex.org/W2170146596","https://openalex.org/W2273267066","https://openalex.org/W2317859901","https://openalex.org/W2329683542","https://openalex.org/W2346950316","https://openalex.org/W2553042643","https://openalex.org/W2554396881","https://openalex.org/W2579434750","https://openalex.org/W2594183968","https://openalex.org/W2769032875","https://openalex.org/W2790385355","https://openalex.org/W2802868704","https://openalex.org/W2805643613","https://openalex.org/W2807018623","https://openalex.org/W2808884084","https://openalex.org/W2809156537","https://openalex.org/W2892229719","https://openalex.org/W2896002881","https://openalex.org/W2901759398","https://openalex.org/W2923013982","https://openalex.org/W2940524715","https://openalex.org/W2946099214","https://openalex.org/W2951624434","https://openalex.org/W2960557205","https://openalex.org/W2968848985","https://openalex.org/W2972401572","https://openalex.org/W2972497960","https://openalex.org/W2979948016","https://openalex.org/W2990691215","https://openalex.org/W2990827591","https://openalex.org/W2999554466","https://openalex.org/W3000600836","https://openalex.org/W3003257820","https://openalex.org/W3004260451","https://openalex.org/W3006508031","https://openalex.org/W3007329471","https://openalex.org/W3009999522","https://openalex.org/W3024638960","https://openalex.org/W3032922645","https://openalex.org/W3033000020","https://openalex.org/W3042221936","https://openalex.org/W3046615517","https://openalex.org/W3091756663","https://openalex.org/W3093030756","https://openalex.org/W3094280424","https://openalex.org/W3097857367","https://openalex.org/W3109716390","https://openalex.org/W3120408379","https://openalex.org/W3121372797","https://openalex.org/W3123655913","https://openalex.org/W3125008742","https://openalex.org/W3127559895","https://openalex.org/W3128618129","https://openalex.org/W3134520508","https://openalex.org/W3136592363","https://openalex.org/W3148071990","https://openalex.org/W3157191457","https://openalex.org/W3164288609","https://openalex.org/W3167140978","https://openalex.org/W3170186615","https://openalex.org/W3174122508","https://openalex.org/W3176005660","https://openalex.org/W3192134500","https://openalex.org/W3193511962","https://openalex.org/W3195900569","https://openalex.org/W3196073854","https://openalex.org/W3196609471","https://openalex.org/W3198205651","https://openalex.org/W3199401237","https://openalex.org/W3204371732","https://openalex.org/W3216149451","https://openalex.org/W4200140951","https://openalex.org/W4205167633","https://openalex.org/W4205478771","https://openalex.org/W4205838221","https://openalex.org/W4206501154","https://openalex.org/W4206547282","https://openalex.org/W4220734682","https://openalex.org/W4225264311","https://openalex.org/W4226373709","https://openalex.org/W4229332892","https://openalex.org/W4229371438","https://openalex.org/W4280492560","https://openalex.org/W4280653996","https://openalex.org/W4281922383","https://openalex.org/W4289656533","https://openalex.org/W4291008360","https://openalex.org/W4293219024","https://openalex.org/W4294783533","https://openalex.org/W4296639080","https://openalex.org/W4296777868","https://openalex.org/W4297458751","https://openalex.org/W4308510076","https://openalex.org/W4308690706","https://openalex.org/W4311068048","https://openalex.org/W4313503600","https://openalex.org/W4313555682","https://openalex.org/W4318624508","https://openalex.org/W4366577362","https://openalex.org/W4367049415","https://openalex.org/W4367054091","https://openalex.org/W4377289963","https://openalex.org/W4386758612","https://openalex.org/W4389131658","https://openalex.org/W4389932327","https://openalex.org/W4396584787","https://openalex.org/W4400042185","https://openalex.org/W4400457299","https://openalex.org/W4400589645","https://openalex.org/W4401411045","https://openalex.org/W4401811473","https://openalex.org/W4404599162","https://openalex.org/W4408579100"],"related_works":[],"abstract_inverted_index":{"CANDO":[0],"is":[1,11],"available":[2,12],"at":[3,13],"https://github.com/ram-compbio/CANDO.":[4],"The":[5],"version":[6],"used":[7],"in":[8],"this":[9],"article":[10],"http://compbio.buffalo.edu/data/mc_cando_benchmarking2.":[14]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-11-09T00:00:00"}