The set is based on the ZINC Clean Leads collection. It contains 4,591,276 molecules in total, filtered by molecular weight in the range from 250 to 350 Daltons, a number of rotatable bonds not greater than 7, and XlogP less than or equal to 3.5. We removed molecules containing charged atoms or atoms besides C, N, S, O, F, Cl, Br, H or cycles longer than 8 atoms. The molecules were filtered via medicinal chemistry filters (MCFs) and PAINS filters.
The dataset contains 1,936,962 molecular structures. For experiments, we split the dataset into a training, test and scaffold test sets containing around 1.6M, 176k, and 176k molecules respectively. The scaffold test set contains unique Bemis-Murcko scaffolds that were not present in the training and test sets. We use this set to assess how well the model can generate previously unobserved scaffolds.