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We revised the protocols used to benchmark our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery platform to bring them into strong alignment with best practices.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>CANDO ranked 7.4% and 12.1% of known drugs in the top 10 compounds for their respective diseases\/indications using drug-indication mappings from the Comparative Toxicogenomics Database (CTD) and Therapeutic Targets Database (TTD), respectively. Performance was weakly positively correlated (Spearman correlation coefficient &amp;gt; 0.3) with the number of drugs associated with an indication and moderately correlated (coefficient &amp;gt; 0.5) with intra-indication chemical similarity. There was also a moderate correlation between performance on our original and new benchmarking protocols. Better performance was observed when using TTD instead of CTD when drug-indication associations appearing in both mappings were assessed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CANDO is available at https:\/\/github.com\/ram-compbio\/CANDO. The version used in this article is available at http:\/\/compbio.buffalo.edu\/data\/mc_cando_benchmarking2.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf604","type":"journal-article","created":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T01:35:06Z","timestamp":1762652106000},"source":"Crossref","is-referenced-by-count":2,"title":["Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6190-7381","authenticated-orcid":false,"given":"Melissa","family":"Van Norden","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY 14203,","place":["United 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