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We report a set of scaffolds that occur in NPs (Figure 5) and metabolites (Figure 6), with a minimum Tanimoto similarity of 0.9 to the scaffolds found in drugs, which are actually missing in currently used lead datasets.
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Figure 5 A set of scaffolds present in NPs but are missing in lead dataset.
Figure 6 A set of scaffolds present in metabolites but are missing in lead dataset.
Furthermore, we note that 97.4% of the scaffolds found in lead dataset contain aromatic rings.
We also note that only a small percentage (5%) of natural product scaffolds space is shared by the lead dataset.
For lead dataset, we merged two independent screening sets obtained from BioNET [33] and Maybridge database [34].
We also observe that the lead dataset is well within Lipinski's universe and covers a fair amount of drug space.
We have identified specific scaffolds that are present in metabolites and natural products, with close counterparts in the drugs, but are missing in the lead dataset.
Further, we note that the fragments found in metabolites are least similar to the fragments present in NPs and lead dataset.
We find that of the total 296 non-redundant scaffolds found in metabolites (Table 3), 123 (42%) are shared by drugs whereas only 68 (23%) are shared by the lead dataset.
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CEO of Professional Science Editing for Scientists @ prosciediting.com