Genetic algorithm and Tabu search based methods for molecular 3D-structure prediction

Abdel-Rahman Hedar; Ahmed Fouad Ali; Taysir  Hassan Abdel-Hamid

doi:10.3934/naco.2011.1.191

Article Contents

2011, Volume 1, Issue 1: 191-209. Doi: 10.3934/naco.2011.1.191

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Genetic algorithm and Tabu search based methods for molecular 3D-structure prediction

1.
Dept. of Computer Science, Faculty of Computers and Information, Assiut University, Assiut 71526
2.
Department of Mathematics, Faculty of Science, Assiut University, Assiut, 71516
3.
Department of Information Systems, Faculty of Computers and Information, Assiut University, Assiut, 71526

Received: October 2010

Revised: November 2010

Published: January 2011

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Abstract

The search for the global minimum of a potential energy function is very difficult since the number of local minima grows exponentially with the molecule size. The present work proposes the application of genetic algorithm and tabu search methods, which are called GAMCP (Genetic Algorithm with Matrix Coding Partitioning) [7], and TSVP (Tabu Search with Variable Partitioning) [8], respectively, for minimizing the molecular potential energy function. Computational results for problems with up to 200 degrees of freedom are presented and are favorable compared with other four existing methods from the literature. Numerical results show that the proposed two methods are promising and produce high quality solutions with low computational costs.

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Mathematics Subject Classification: Primary: 92D20, 68T20, 68W20; Secondary: 68T05, 91E40.

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