Protein structure prediction with local adjust tabu search algorithm.
Protein structure prediction with local adjust tabu search algorithm.
复制标题
使用局部调整禁忌搜索算法预测蛋白质结构
DOI：
10.1186/1471-2105-15-s15-s1
复制
发表时间：
2014
影响因子：
3
通讯作者：
Zhou F
中科院分区：
文献类型：
--
作者：
Lin X;Zhang X;Zhou F
背景蛋白质折叠结构预测是生物信息学领域最具挑战性的问题之一。由于现实蛋白质结构的复杂性，在研究中应采用简化的结构模型和计算方法。AB非格点模型是一种简化模型，它只考虑了疏水（A）和亲水（B）两类氨基酸残基。结果本文的主要工作是讨论如何利用Fibonacci序列和真实的蛋白质序列优化二维非格点模型和三维非格点模型中的最低能量构型。为了避免陷入局部最小值和更快地收敛到全局最小值，本文将模拟退火算法与禁忌搜索算法相结合，提出了一种新的求解蛋白质结构问题的方法（SATS）。采用新的编码策略、自适应邻域生成策略和局部调整策略等多种策略，成功地实现了对蛋白质序列能量最低对应的最佳构象的快速搜索。实验结果表明，改进后的SATS模型得到的部分结果优于已有文献报道的结果，并且可以确定找到了短Fibonacci序列的最低能量折叠态. Conclusionsoff-lattice模型虽然不太符合实际，但能够反映实际蛋白质的一些重要特征.结果表明，三维非格点模型比二维非格点模型更接近真实蛋白质的天然折叠结构。此外，与以往的一些研究相比，所提出的混合算法可以更有效，更快地搜索蛋白质链的空间折叠结构。
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.