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Hilbert-Curve Assisted Structure Embedding Method

submitted on 28.02.2020, 00:35 and posted on 28.02.2020, 13:35 by Gergely Zahoranszky-Kohalmi, Kanny K. Wan, Alexander G. Godfrey
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 .


This research was supported by the Intramural research program of the NCATS, NIH.


Email Address of Submitting Author


National Center for Advancing Translational Sciences (NCATS/NIH), Medical Center Dr., Rockville, USA


United States of America

ORCID For Submitting Author


Declaration of Conflict of Interest

The authors declare that they have no competing interests.

Version Notes

Version 1.