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Evolutionary algorithms for automated drug design towards target molecule properties

Authors:

Johannes W. Kruisselbrink,

Thomas Bäck,

Ad P. IJzerman,

Eelke van der HorstAuthors Info & Claims

GECCO '08: Proceedings of the 10th annual conference on Genetic and evolutionary computation

Pages 1555 - 1562

https://doi.org/10.1145/1389095.1389393

Published: 12 July 2008 Publication History

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Abstract

This paper presents an evolutionary algorithm for the automated design of molecules that could be used as drugs. It is designed to provide the medicinal chemist with a number of candidate molecules that comply to pre-defined properties. These candidate molecules can be promising for further evaluation.

The proposed algorithm is implemented as an extension to the so-called Molecule Evoluator [3] which implements an interactive evolutionary algorithm. The Molecule Evoluator is extended with an automated evolutionary algorithm that implements a variable sized population and bases its search on target-bounds that are set for a number of molecule properties. Moreover, the algorithm uses a selection procedure based on the notion of Pareto domination.

The results show that it is indeed possible to apply the concept of evolutionary computation on automated molecule design using target-bounds for molecule properties as optimization goals. For practical usage, the presented algorithm could serve as a starting point, but should be further improved with respect to diversity within the generated set of molecules.

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Cited By

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Lücken CBarán BBrizuela C(2014)A survey on multi-objective evolutionary algorithms for many-objective problemsComputational Optimization and Applications10.1007/s10589-014-9644-158:3(707-756)Online publication date: 1-Jul-2014
https://dl.acm.org/doi/10.1007/s10589-014-9644-1
Bajaj CChowdhury RRasheed MBronsvoort WGonsor DRegli WGrandine TVandenbrande JGravesen JKeyser J(2009)A dynamic data structure for flexible molecular maintenance and informatics2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling10.1145/1629255.1629287(259-270)Online publication date: 5-Oct-2009
https://dl.acm.org/doi/10.1145/1629255.1629287
Kruisselbrink JAleman AEmmerich MIJzerman ABender ABaeck Tvan der Horst ERothlauf F(2009)Enhancing search space diversity in multi-objective evolutionary drug molecule design using nichingProceedings of the 11th Annual conference on Genetic and evolutionary computation10.1145/1569901.1569932(217-224)Online publication date: 8-Jul-2009
https://dl.acm.org/doi/10.1145/1569901.1569932
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Index Terms

Evolutionary algorithms for automated drug design towards target molecule properties
1. Applied computing
  1. Physical sciences and engineering
    1. Chemistry

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GECCO '08: Proceedings of the 10th annual conference on Genetic and evolutionary computation

July 2008

1814 pages

ISBN:9781605581309

DOI:10.1145/1389095

Conference Chair:
Conor Ryan
University of Limerick, Ireland
,
Editor:
Maarten Keijzer
Chordiant Software International B.V., The Netherlands

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Published: 12 July 2008

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GECCO08: Genetic and Evolutionary Computation Conference

July 12 - 16, 2008

GA, Atlanta, USA

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Lücken CBarán BBrizuela C(2014)A survey on multi-objective evolutionary algorithms for many-objective problemsComputational Optimization and Applications10.1007/s10589-014-9644-158:3(707-756)Online publication date: 1-Jul-2014
https://dl.acm.org/doi/10.1007/s10589-014-9644-1
Bajaj CChowdhury RRasheed MBronsvoort WGonsor DRegli WGrandine TVandenbrande JGravesen JKeyser J(2009)A dynamic data structure for flexible molecular maintenance and informatics2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling10.1145/1629255.1629287(259-270)Online publication date: 5-Oct-2009
https://dl.acm.org/doi/10.1145/1629255.1629287
Kruisselbrink JAleman AEmmerich MIJzerman ABender ABaeck Tvan der Horst ERothlauf F(2009)Enhancing search space diversity in multi-objective evolutionary drug molecule design using nichingProceedings of the 11th Annual conference on Genetic and evolutionary computation10.1145/1569901.1569932(217-224)Online publication date: 8-Jul-2009
https://dl.acm.org/doi/10.1145/1569901.1569932
Kruisselbrink JEmmerich MBäck TBender AIjzerman AHorst E(2009)Combining Aggregation with Pareto OptimizationProceedings of the 5th International Conference on Evolutionary Multi-Criterion Optimization10.1007/978-3-642-01020-0_36(453-467)Online publication date: 21-Apr-2009
https://dl.acm.org/doi/10.1007/978-3-642-01020-0_36

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Evolutionary Algorithms in Drug Design

Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching

Structure based drug design studies on urokinase plasminogen activator inhibitors using AutoDock

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