Title: Scatter Search algorithm for Protein Structure Prediction

Authors: Nashat Mansour, Christine Kehyayan, Hassan Khachfe

Addresses: Department of Computer Science and Mathematics, Lebanese American University, 1102 2801, Lebanon. ' Department of Computer Science and Mathematics, Lebanese American University, 1102 2801, Lebanon; Department of Computer Science and Software Engineering, Concordia University, H3G 1M8, Canada. ' Department of Biology and Biomedical Sciences, Lebanese International University, 2049 5508, Lebanon

Abstract: In this paper, we present a Scatter Search (SS) algorithm for predicting 3D structures of proteins based on torsion angles representation. Given the protein|s sequence of Amino Acids (AAs), our algorithm produces a 3D structure that aims to minimise the energy function associated with the structure. SS is an evolutionary approach that is based on a population of candidate solutions. These candidates undergo evolutionary operations that combine search intensification and diversification over a number of iterations. We evaluate our algorithm on three proteins taken from a Protein Data Bank (PDB). The results show that our algorithm is able to produce 3D structures with good sub-optimal energy values. Also, the Root Mean Square Deviations (RMSD) of these structures from the reference proteins are promising within limits imposed by the assumptions made.

Keywords: ab initio approach; torsion angles; protein structure prediction; scatter search; bioinformatics; amino acids.

DOI: 10.1504/IJBRA.2009.028679

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.5, pp.501 - 515

Published online: 22 Sep 2009 *

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