Numerical Algebra, Control and Optimization (NACO)

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

Pages: 191 - 209, Volume 1, Issue 1, March 2011      doi:10.3934/naco.2011.1.191

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Abdel-Rahman Hedar - Dept. of Computer Science, Faculty of Computers and Information, Assiut University, Assiut 71526, Egypt (email)
Ahmed Fouad Ali - Department of Mathematics, Faculty of Science, Assiut University, Assiut, 71516, Egypt (email)
Taysir Hassan Abdel-Hamid - Department of Information Systems, Faculty of Computers and Information, Assiut University, Assiut, 71526, Egypt (email)

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.

Keywords:  Genetic algorithm, tabu search, potential energy functions, global optimization.
Mathematics Subject Classification:  Primary: 92D20, 68T20, 68W20; Secondary: 68T05, 91E40.

Received: October 2010;      Revised: November 2010;      Available Online: February 2011.