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