A consensus compound/bioactivity dataset for data-driven drug design and chemogenomics

  • Publicly available compound and bioactivity databases provide an essential basis for data-driven applications in life-science research and drug design. By analyzing several bioactivity repositories, we discovered differences in compound and target coverage advocating the combined use of data from multiple sources. Using data from ChEMBL, PubChem, IUPHAR/BPS, BindingDB, and Probes & Drugs, we assembled a consensus dataset focusing on small molecules with bioactivity on human macromolecular targets. This allowed an improved coverage of compound space and targets, and an automated comparison and curation of structural and bioactivity data to reveal potentially erroneous entries and increase confidence. The consensus dataset comprised of more than 1.1 million compounds with over 10.9 million bioactivity data points with annotations on assay type and bioactivity confidence, providing a useful ensemble for computational applications in drug design and chemogenomics.

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Author:Laura IsigkeitORCiD, Apirat ChaikuadORCiD, Daniel MerkORCiDGND
Parent Title (English):Molecules
Place of publication:Basel
Document Type:Article
Date of Publication (online):2022/04/13
Date of first Publication:2022/04/13
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/11/21
Tag:big data; data curation; de novo design; machine learning; medicinal chemistry
Issue:8, art. 2513
Article Number:2513
Page Number:13
First Page:1
Last Page:13
This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No. 875510. The JU receives support from the European Union’s Horizon 2020 research and innovation program, EFPIA, Ontario Institute for Cancer Research, Royal Institution for the Advancement of Learning McGill University, Kungliga Tekniska Hoegskolan, and Diamond Light Source Limited.
The consensus dataset generated and analyzed in this study is freely available from Zenodo (https://zenodo.org), with the doi:10.5281/zenodo.6398019.
Institutes:Biochemie, Chemie und Pharmazie
Fachübergreifende Einrichtungen / Buchmann Institut für Molekulare Lebenswissenschaften (BMLS)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften
Licence (German):License LogoCreative Commons - CC BY - Namensnennung 4.0 International