title: A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding.
abstract: The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model. The proposed HE-L-PSO algorithm exhibited favorable performance in predicting both short and long amino acid sequences with high reproducibility and stability, compared with seven reported algorithms. The HE-L-PSO algorithm yielded optimal solutions for all predicted protein folding structures. All HE-L-PSO-predicted protein folding structures possessed a hydrophobic core that is similar to normal protein folding.
authors.affiliation: 1 Department of Electronic Engineering, National Kaohsiung University of Applied Sciences , Kaohsiung, Taiwan .
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.affiliation: 1 Department of Electronic Engineering, National Kaohsiung University of Applied Sciences , Kaohsiung, Taiwan .
authors.forename: Yu-Shiun
authors.initials: YS
authors.lastname: Lin
authors.affiliation: 2 Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I-Shou University , Kaohsiung, Taiwan .
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.affiliation: 3 Institute of Medical Science and Technology, National Sun Yat-sen University , Kaohsiung, Taiwan .|4 Department of Medical Research, Kaohsiung Medical University Hospital , Kaohsiung, Taiwan .|5 Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University , Kaohsiung, Taiwan .
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results
chemical_list: D011506:Proteins
keywords: global search; hydrophobic-polar (HP) model; local search; particle swarm optimization; protein folding