The molecule evoluator: an interactive evolutionary algorithm for designing drug molecules

Authors:
Eric-Wubbo Lameijer;Ad IJzerman;Joost Kok
Affiliations:
Leiden University, Leiden, the Netherlands;Leiden University, Leiden, the Netherlands;Leiden University, Leiden, the Netherlands
Venue:
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Year:
2005

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Abstract

To help chemists design new drugs, we created a tool that uses interactive evolution to design drug molecules, the "Molecule Evoluator". In contrast to most other evolutionary de novo design programs, the molecule representation and the set of mutations enable it to both search the chemical space of all drug like molecules extensively and to fine-tune molecular structures to the problem at hand. Additionally, we use interaction with the user as a fitness function, which is new in evolutionary algorithms in drug design. This interactivity allows the Molecule Evoluator to use the domain knowledge of the chemist to estimate the ease of synthesis and the biological activity of the compound. This knowledge can guide the optimization process and thereby improve its results. Chemists of our department using the Molecule Evoluator were able to find six novel and synthesizable druglike core structures, indicating that the Molecule Evoluator can be used as a tool to enhance the chemist's creativity.