A Quasi-physical Algorithm for the Structure Optimization in an Off-lattice Protein Model  

作　　者：Jing-Fa Liu Wen-Qi Huang 

机构地区：[1]School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China [2]Department of Mathematics, Hengyang Normal College, Hengyang 421008, China

出　　处：《Genomics, Proteomics & Bioinformatics》2006年第1期61-66,共6页基因组蛋白质组与生物信息学报（英文版）

摘　　要：In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.

关 键 词：protein folding off-lattice model quasi-physical algorithm off-trap strategy 

分 类 号：Q51[生物学—生物化学]