title: A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides.
abstract: The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone dihedral angles of conformations of amino acids (AAs) and dipeptides is performed. The structural information is used to design a new encoding scheme to improve the efficiency of GA search. Local geometry optimizations based on the energy calculations by the density functional theory are employed to safeguard the quality and reliability of the GA structures. The GA scheme is applied to the conformational searches of Lys, Arg, Met-Gly, Lys-Gly, and Phe-Gly-Gly representative of AAs, dipeptides, and tripeptides with complicated side chains. Comparison with the best literature results shows that the new GA method is both highly efficient and reliable by providing the most complete set of the low energy conformations. Moreover, the computational cost of the GA method increases only moderately with the complexity of the molecule. The GA scheme is valuable for the study of the conformations and properties of oligopeptides. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ru
authors.affiliation: Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China.
authors.forename: Ce
authors.initials: C
authors.lastname: Song
authors.affiliation: Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China.|Department of Physics, University of Science and Technology of China, Hefei, 230026, China.
authors.forename: Zijing
authors.initials: Z
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008957:Models, Genetic; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D000596:Amino Acids; D004151:Dipeptides; D009842:Oligopeptides
keywords: conformational coverage; dihedral angle; geometry optimization; potential energy surface; structural prediction