The State of the Art on Chemical Databases and Libraries

Stepanić, Višnja; Hršak, Dalibor; Kobetić, Renata (2024) The State of the Art on Chemical Databases and Libraries. Croatica Chemica Acta, 97 (4). P1-P12. ISSN 00111643

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Abstract

Molecules that act on the biological target at micromolar level at least are called hits. The usual method for identifying hits is high-throughput screening (HTS) of chemical libraries in relevant in vitro assays. An even more efficient, cost-effective and faster method for identifying hits is to perform virtual pre-screening, where the top scoring hits are validated in appropriate in vitro assays. Both wet HTS and virtual screening using structure- or ligand-based approaches utilise large libraries containing millions to billions of drug-like compounds. In this paper, we provide an insight into the state of the art in large collections of small molecular weight molecules, i) public databases for synthetic compounds (PubChem, ChEMBL) and natural products (COCONUT, LOTUS) and commercial ultra-large chemical libraries, ii) make-on-demand virtual libraries (Enamine, Galaxi®, ZINC-22) and iii) wet DNA-encoded libraries (DELs). Machine learning methods for characterising and visualising molecular diversity in screening collections are also described.

Item Type:	Article
Uncontrolled Keywords:	database; library; ultra-large library; DNA-encoded library; virtual screening; hits; machine learning; visualization; PCA; t-SNE; UMAP
Subjects:	NATURAL SCIENCES > Chemistry
Divisions:	Division of Electronics
Depositing User:	Sanja Jurković
Date Deposited:	17 Apr 2025 11:46
URI:	http://fulir.irb.hr/id/eprint/9706
DOI:	10.5562/cca4130

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