Predicting the non-compact conformation of amino acid sequence by particle swarm optimization

摘要：

　　Hydrophobic-hydrophilic (HP) model serves as a surrogate for the protein structure prediction problem to fold a chain of amino acids into a 2D square lattice.By the fact that the number of amino acids is equal to the number of lattice points or not,there are two types of folding conformations,i.e.,the compact and non-compact conformations.Non-compact conformation tries to fold the amino acids sequence into a relatively larger square lattice,which is more biologically realistic and significant than the compact conformation.Here,we propose a heuristic algorithm to predict the non-compact conformations in 2D HP model.First,the protein structure prediction problem is abstracted to match amino acids to lattice points.The problem is then formulated as an integer programming model and we transform the biological problem into an optimization problem.Classical particle swarm optimization algorithm is extended by the single point adjustment strategy to solve this problem.Compared with existing self-organizing map algorithm,our method is more effective in several benchmark examples.

关键词： Protein structure prediction Non-compact conformation HP lattice model Particle swarm optimization

作者: Yuzhen Guo Yong Wang

作者单位: Department of MathematicsNanjing University of Aeronautics and AstronauticsNanjing, China Academy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing, China

会议类型: 国际会议

会议名称: 7th International Conference on Systems Biology(第7届计算系统生物学国际研讨会)(ISB2013)

会议地点: 安徽黄山

会议语种:英文

页码: 119-122

在线出版日期: 2013-08-22（万方平台首次上网日期，不代表论文的发表时间）