Fig. 4. Percentage of the most common scaffolds after training with each method for PPARδ. The most common scaffolds of the PPARδ fine-tuning sets were determined, and for each method, the percentage of the matched scaffold of the 4000 designs was calculated for different dataset sizes (a and c: 10; b and d: 100) and similarity levels (a and b: high; c and d: low). The most common scaffolds are visualized above every graph with the percentage of its occurrence in the fine-tuning set. The analysis for PIM and JAK2 can be found in Supporting Fig. S6 and S7, respectively.