Quasi-physical Algorithm for Protein Folding in an Off-Lattice Model

作     者：Lü Zhi-Peng HUANG Wen-Qi SHI He 

作者机构：School of Computer Science and Technology Huazhong University of Science and Technology Wuhan 430074 China Academy of Mathematics and Systems Sciences the Chinese Academy of Sciences Beijing 100080 China 

出 版 物：《Communications in Theoretical Physics》 (理论物理通讯（英文版）)

年 卷 期：2007年第47卷第1期

页      面：181-185页

核心收录：

学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 

基　　金：The project partially supported by National Key Basic Research Project of China under Grant No. 2004GB318000 and National Natural Science Foundation of China under Grant No. 10471051 

主　　题：quasi-physical algorithm conjugate gradient method protein folding off-lattice model 

摘      要：We study a three-dimensional off-lattice protein folding model, which involves two species of residues interacting through Lennard-Jones potentials. By incorporating an extra energy contribution into the original potential function, we replace the original constrained problem with an unconstrained minimization of a mixed potential function. As such an efficient quasi-physical algorithm for solving the protein folding problem is presented. We apply the proposed algorithm to sequences with up to 55 residues and compare the computational results with the putative lowest energy found by several of the most famous algorithms, showing the advantages of our method. The dynamic behavior of the quasi-physlcal algorithm is also discussed.