Scatter search algorithm for protein structure prediction.
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.
Mansour
Nashat
N
Department of Computer Science and Mathematics, Lebanese American University, Lebanon. nmansour@lau.edu.lb
Kehyayan
Christine
C
Khachfe
Hassan
H
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins