Publication
Title
A molecule perturbation software library and its application to study the effects of molecular design constraints
Author
Abstract
Computational molecular design can yield chemically unreasonable compounds when performed carelessly. A popular strategy to mitigate this risk is mimicking reference chemistry. This is commonly achieved by restricting the way in which molecules are constructed or modified. While it is well established that such an approach helps in designing chemically appealing molecules, concerns about these restrictions impacting chemical space exploration negatively linger. In this work we present a software library for constrained graph-based molecule manipulation and showcase its functionality by developing a molecule generator. Said generator designs molecules mimicking reference chemical features of differing granularity. We find that restricting molecular construction lightly, beyond the usual positive effects on drug-likeness and synthesizability of designed molecules, provides guidance to optimization algorithms navigating chemical space. Nonetheless, restricting molecular construction excessively can indeed hinder effective chemical space exploration.
Language
English
Source (journal)
Journal of Cheminformatics
Publication
2023
ISSN
1758-2946
DOI
10.1186/S13321-023-00761-5
Volume/pages
15 (2023) , p. 1-17
Article Reference
89
ISI
001070929000001
Pubmed ID
37752561
Medium
E-only publicatie
Full text (Publisher's DOI)
Full text (open access)
UAntwerpen
Faculty/Department
Research group
Publication type
Subject
Affiliation
Publications with a UAntwerp address
External links
Web of Science
Record
Identifier
Creation 27.09.2023
Last edited 25.04.2024
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