Extracting Compound Profiling Matrices from Screening Data

ACS Omega
Martin VogtJürgen Bajorath

Abstract

Compound profiling matrices record assay results for compound libraries tested against panels of targets. In addition to their relevance for exploring structure-activity relationships, such matrices are of considerable interest for chemoinformatic and chemogenomic applications. For example, profiling matrices provide a valuable data resource for the development and evaluation of machine learning approaches for multitask activity prediction. However, experimental compound profiling matrices are rare in the public domain. Although they are generated in pharmaceutical settings, they are typically not disclosed. Herein, we present an algorithm for the generation of large profiling matrices, for example, containing more than 100 000 compounds exhaustively tested against 50 to 100 targets. The new methodology is a variant of biclustering algorithms originally introduced for large-scale analysis of genomics data. Our approach is applied here to assays from the PubChem BioAssay database and generates profiling matrices of increasing assay or compound coverage by iterative removal of entities that limit coverage. Weight settings control final matrix size by preferentially retaining assays or compounds. In addition, the methodology can a...Continue Reading

References

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Aug 10, 2002·Bioinformatics·Amos TanayRon Shamir
Sep 10, 2008·Nature Biotechnology·Jordi MestresRicard V Solé
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Oct 11, 2010·Molecular Informatics·Yusuf TanrikuluHans-Marcus Bitter
Dec 1, 2013·Molecular Informatics·Jürgen Bajorath
Dec 3, 2016·Nucleic Acids Research·Yanli WangJian Zhang
Jul 20, 2018·ACS Omega·Raquel Rodríguez-PérezJürgen Bajorath

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Citations

Jan 23, 2020·Expert Opinion on Drug Discovery·Karina Martinez-MayorgaGerald Maggiora
Oct 4, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gerhard Hessler, Karl-Heinz Baringhaus
Oct 3, 2018·Future Science OA·Martin VogtJürgen Bajorath
Nov 30, 2019·Future Medicinal Chemistry·Albert A AntolinBissan Al-Lazikani
Jul 20, 2018·ACS Omega·Raquel Rodríguez-PérezJürgen Bajorath

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Methods Mentioned

BETA
Assay

Software Mentioned

PubChem
ZINC
ChEMBL

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