Hilbert-Curve Assisted Structure Embedding Method

This work introduces a novel chemical space embedding method "Hilbert-Curve Assisted Structure Embedding (HCASE)" with help of pseudo-Hilbert Curves and Scaffold- Keys. The method was designed to produce an embedding that can be intuitively interpreted by medicinal chemists and data analysts. We analyzed the embedding of approved drug molecules (DrugBank) and natural products (CANVASS) into chemical spaces defined by Bemis-Murcko scaffolds extracted from ChEMBL (v24.1) database and from ChEMBL (v23) Natural Products. The implementation of HCASE algorithm and the input and results files of the analyses are available at https://github.com/ncats/hcase .