A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules

With enormous success in both science and engineering, the recent advances in evolutionary computation—particularly memetic computing—is gaining increasing attention in the molecular optimization community. In this paper, our interest is to introduce a memetic computational methodology for the disco...

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Main Authors: Ellabaan, Mostafa Mostafa Hashim, Handoko, Stephanus Daniel, Ong, Yew Soon, Kwoh, Chee Keong, Bahnassy, S. A., Elassawy, F. M., Man, H. Y.
Other Authors: School of Computer Engineering
Format: Article
Language:English
Published: 2013
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Online Access:https://hdl.handle.net/10356/97363
http://hdl.handle.net/10220/13134
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-973632020-05-28T07:41:34Z A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules Ellabaan, Mostafa Mostafa Hashim Handoko, Stephanus Daniel Ong, Yew Soon Kwoh, Chee Keong Bahnassy, S. A. Elassawy, F. M. Man, H. Y. School of Computer Engineering DRNTU::Engineering::Computer science and engineering With enormous success in both science and engineering, the recent advances in evolutionary computation—particularly memetic computing—is gaining increasing attention in the molecular optimization community. In this paper, our interest is to introduce a memetic computational methodology for the discovery of low-energy stable conformations—also known as the stereoisomers—of covalently-bonded molecules, due to the abundance of such molecules in nature and their importance in biology and chemistry. To an optimization algorithm, maintaining the same set of bonds over the course of searching for the stereoisomers is a great challenge. Avoiding the steric effect, i.e. preventing atoms from overlapping or getting too close to each other, is another challenge of molecular optimization. Addressing these challenges, three novel nature-inspired tree-based evolutionary operators are first introduced in this paper. A tree-structured covalent-bond-driven molecular memetic algorithm (TCM-MA)—tailored specifically to deal with molecules that involve covalent bonding but contain no cyclic structures using the three novel evolutionary operators—is then proposed for the efficient search of the stereoisomers of ring-deficient covalently-bonded molecules. Through empirical study using the glutamic acid as a sample molecule of interest, it is witnessed that the proposed TCM-MA discovered as many as up to sixteen times more stereoisomers within as little as up to a five times tighter computational budget compared to two other state-of-the-art algorithms. 2013-08-15T08:16:41Z 2019-12-06T19:41:53Z 2013-08-15T08:16:41Z 2019-12-06T19:41:53Z 2012 2012 Journal Article Ellabaan, M. M. H., Handoko, S., Ong, Y., Kwoh, C., Bahnassy, S., Elassawy, F., & Man, H. (2012). A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules. Computers & mathematics with applications, 64(12), 3792-3804. 0898-1221 https://hdl.handle.net/10356/97363 http://hdl.handle.net/10220/13134 10.1016/j.camwa.2012.02.055 en Computers & mathematics with applications
institution Nanyang Technological University
building NTU Library
country Singapore
collection DR-NTU
language English
topic DRNTU::Engineering::Computer science and engineering
spellingShingle DRNTU::Engineering::Computer science and engineering
Ellabaan, Mostafa Mostafa Hashim
Handoko, Stephanus Daniel
Ong, Yew Soon
Kwoh, Chee Keong
Bahnassy, S. A.
Elassawy, F. M.
Man, H. Y.
A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
description With enormous success in both science and engineering, the recent advances in evolutionary computation—particularly memetic computing—is gaining increasing attention in the molecular optimization community. In this paper, our interest is to introduce a memetic computational methodology for the discovery of low-energy stable conformations—also known as the stereoisomers—of covalently-bonded molecules, due to the abundance of such molecules in nature and their importance in biology and chemistry. To an optimization algorithm, maintaining the same set of bonds over the course of searching for the stereoisomers is a great challenge. Avoiding the steric effect, i.e. preventing atoms from overlapping or getting too close to each other, is another challenge of molecular optimization. Addressing these challenges, three novel nature-inspired tree-based evolutionary operators are first introduced in this paper. A tree-structured covalent-bond-driven molecular memetic algorithm (TCM-MA)—tailored specifically to deal with molecules that involve covalent bonding but contain no cyclic structures using the three novel evolutionary operators—is then proposed for the efficient search of the stereoisomers of ring-deficient covalently-bonded molecules. Through empirical study using the glutamic acid as a sample molecule of interest, it is witnessed that the proposed TCM-MA discovered as many as up to sixteen times more stereoisomers within as little as up to a five times tighter computational budget compared to two other state-of-the-art algorithms.
author2 School of Computer Engineering
author_facet School of Computer Engineering
Ellabaan, Mostafa Mostafa Hashim
Handoko, Stephanus Daniel
Ong, Yew Soon
Kwoh, Chee Keong
Bahnassy, S. A.
Elassawy, F. M.
Man, H. Y.
format Article
author Ellabaan, Mostafa Mostafa Hashim
Handoko, Stephanus Daniel
Ong, Yew Soon
Kwoh, Chee Keong
Bahnassy, S. A.
Elassawy, F. M.
Man, H. Y.
author_sort Ellabaan, Mostafa Mostafa Hashim
title A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
title_short A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
title_full A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
title_fullStr A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
title_full_unstemmed A tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
title_sort tree-structured covalent-bond-driven molecular memetic algorithm for optimization of ring-deficient molecules
publishDate 2013
url https://hdl.handle.net/10356/97363
http://hdl.handle.net/10220/13134
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