Related Experiment Video
Updated: Jan 11, 2026
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
Published on: December 1, 2020
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms
Melissa Van Norden1, William Mangione1, Zackary Falls1
1Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, United States.
Motivation:
Benchmarking is essential for the improvement and comparison of drug discovery platforms. 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.
Results:
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 > 0.3) with the number of drugs associated with an indication and moderately correlated (coefficient > 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.
Availability And Implementation:
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.
