3D protein peptide chain search using an improved genetic algorithm

Abstract

In this paper, an efficient searching algorithm, namely intergeneration projection micro genetic algorithm (IP-μGA) is introduced to search the three dimensional protein conformations. A bond rotation model is developed, in which variables are the dihedral angles along peptide main chain. The root mean square deviation (RMSD) is adopted as the fitness function in the searching process and the template protein structures in protein data bank (PDB) are used for comparison. The results of 3D peptide structures of examples show the effectiveness of present method. © Springer-Verlag Berlin Heidelberg 2003.