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Hilbert-Curve Assisted Structure Embedding Method

preprint
submitted on 28.02.2020 and posted on 28.02.2020 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 https://github.com/ncats/hcase .

Funding

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

History

Email Address of Submitting Author

gzahoranszky@gmail.com

Institution

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

Country

United States of America

ORCID For Submitting Author

0000-0002-2534-8770

Declaration of Conflict of Interest

The authors declare that they have no competing interests.

Version Notes

Version 1.

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