Heuristic algorithm for off-lattice protein folding problem  

作　　者：陈矛 黄文奇 

机构地区：[1]School of Computer Science and Technology, Huazhong University of Science and Technology,Wuhan 430074, China

出　　处：《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》2006年第1期7-12,共6页浙江大学学报（英文版）B辑（生物医学与生物技术）

基　　金：Project supported by the National Basic Research Program (973) of China (No. 2004CB318000) and the National Natural Science Foun-dation of China (No. 10471051)

摘　　要：Enlightened by the law of interactions among objects in the physical world, we propose a heuristic algorithm for solving the three-dimensional (3D) off-lattice protein folding problem. Based on a physical model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem which can be solved by the well-known gra- dient method. To improve the efficiency of our algorithm, a strategy was introduced to generate initial configuration. Computa- tional results showed that this algorithm could find states with lower energy than previously proposed ground states obtained by nPERM algorithm for all chains with length ranging from 13 to 55.Enlightened by the law of interactions among objects in the physical world, we propose a heuristic algorithm for solving the three-dimensional （3D） off-lattice protein folding problem. Based on a physical model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem which can be solved by the well-known gradient method. To improve the efficiency of our algorithm, a strategy was introduced to generate initial configuration. Computational results showed that this algorithm could find states with lower energy than previously proposed ground states obtained by nPERM algorithm for all chains with length ranging from 13 to 55.

关 键 词：Protein folding AB off-lattice model Gradient method 

分 类 号：TP301.6[自动化与计算机技术—计算机系统结构]