title: 3D protein structure prediction using Imperialist Competitive algorithm and half sphere exposure prediction.
abstract: Predicting the native structure of proteins based on half-sphere exposure and contact numbers has been studied deeply within recent years. Online predictors of these vectors and secondary structures of amino acids sequences have made it possible to design a function for the folding process. By choosing variant structures and directs for each secondary structure, a random conformation can be generated, and a potential function can then be assigned. Minimizing the potential function utilizing meta-heuristic algorithms is the final step of finding the native structure of a given amino acid sequence. In this work, Imperialist Competitive algorithm was used in order to accelerate the process of minimization. Moreover, we applied an adaptive procedure to apply revolutionary changes. Finally, we considered a more accurate tool for prediction of secondary structure. The results of the computational experiments on standard benchmark show the superiority of the new algorithm over the previous methods with similar potential function.
authors.affiliation: Graduate Student, Department of Complex Adaptive Systems, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Erfan
authors.initials: E
authors.lastname: Khaji
authors.affiliation: Department of Bio-Chemistry, Iran Military University of Medical Sciences, West Fatemy St, North Karegar Ave, Tehran, Iran.
authors.forename: Masoumeh
authors.initials: M
authors.lastname: Karami
authors.affiliation: Department of Chemistry, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran. Electronic address: z_garkani@uk.ac.ir.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Garkani-Nejad
mesh_terms: D000465:Algorithms; D011237:Predictive Value of Tests; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins
keywords: Half sphere exposure; Imperialist Competitive algorithm; Protein structure prediction; Secondary structure