Protein structure prediction with local adjust tabu search algorithm

BMC Bioinformatics

Proceedings

Xiaolong Zhang¹  Xiaoli Lin²  Fengli zhou³ 

[1] Hubei Key Laboratory of Intelligent Information Processing and Real-time Industrial System, School of Computer Science and Technology, Wuhan University of Science and Technology, 430065, Wuhan, P.R.China;Hubei Key Laboratory of Intelligent Information Processing and Real-time Industrial System, School of Computer Science and Technology, Wuhan University of Science and Technology, 430065, Wuhan, P.R.China;Information and Engineering Department of City College, Wuhan University of Science and Technology, 430065, Wuhan, P.R.China;Information and Engineering Department of City College, Wuhan University of Science and Technology, 430065, Wuhan, P.R.China;

关键词: Tabu Search;    Bovine Spongiform Encephalopathy;    Tabu List;    Tabu Search Algorithm;    Fibonacci Sequence;   

DOI  :  10.1186/1471-2105-15-S15-S1

来源: Springer

【 摘 要 】

BackgroundProtein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues.ResultsThe main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found.ConclusionsAlthough the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain.

【 授权许可】

Unknown   
© Lin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.