Fig. 2

Benchmark and comparison of MicrobeRX with BioTransformer, DrugBank metabolites, and MiMeDB. a Number of orally administered drugs (485) correctly predicted by BioTransformer (81) and MicrobeRX (321). b Number of drug metabolites (1274) correctly predicted by BioTransformer (98) and by MicrobeRX (812). c Molecular weight vs. LogP comparison for predicted metabolites and DrugBank and MiMeDB metabolites. d Principal component analysis (PCA) of molecular similarity between the predictive tools and metabolite datasets using Morgan fingerprints (2048 bits, radius ≥ 2). Duplicated molecules were removed from each dataset prior to comparison. e Number of drugs predicted to be metabolized by microbial or human reactions (barplot at left) and number of metabolites per drug produced per tool (violin plot at right). f Number of unique metabolic structures produced for microbial and human reactions (barplot at left) and the frequency at which each metabolite is predicted (violin plot at right). g Number of unique microbial and human enzyme annotations used for the predictions (barplot at left) and the frequency at which each enzyme is found in the predictions (violin plot at right). In the bar plots in panels e–g, the red bar indicates MicrobeRX predictions and the blue bar indicates BioTransformer predictions