蛋白质折叠的非格子模型

计算物理 ›› 2007, Vol. 24 ›› Issue (2): 234-238.

蛋白质折叠的非格子模型

谭晓超, 何红波, 李义兵

中南大学物理科学与技术学院, 湖南长沙 410083

收稿日期:2005-12-08 修回日期:2006-04-08 出版日期:2007-03-25 发布日期:2007-03-25
作者简介:谭晓超(198l-),湖南衡阳,硕士生,从事生物信息学、生物物理学的研究.
基金资助:
国家自然科学基金(批准号:60371046)资助项目

Off-lattice Model for Protein Folding

TAN Xiaochao, HE Hongbo, LI Yibing

Sehool ofPhysics, Central South University, Changsha 410083, China

Received:2005-12-08 Revised:2006-04-08 Online:2007-03-25 Published:2007-03-25

摘要/Abstract

摘要： 用粒子群算法对蛋白质的简化模型进行研究,体系中各原子间的相互作用由一物理势表示.通过全局优化体系的势函数得到蛋白质的结构数据,与实验测得的结构数据之间的均方根偏差RMSD为6.12Å.记录了能量最小值及回转半径随程序运行步骤的变化以及RMSD值与最低能量值的分布关系,这些结果反映了蛋白质折叠的一些基本特征.

关键词: 非格子模型, PSO算法, 蛋白质折叠

Abstract: A simplified off-lattice model of protein is studied with a PSO algorithm.Interaction between atoms is represented by a physical-based potential.The protein's RMSD value between computed and experimental structures is 6.12Å in optimizing the potential in global space. The protein total energy and radius of gyration at PSO steps and the relation between minimum energy and corresponding RMSD value are investigated.It shows basic characteristics of protein folding.

Key words: off-lattice model, PSO algorithm, protein folding

中图分类号:

Q1615

谭晓超, 何红波, 李义兵. 蛋白质折叠的非格子模型[J]. 计算物理, 2007, 24(2): 234-238.

TAN Xiaochao, HE Hongbo, LI Yibing. Off-lattice Model for Protein Folding[J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2007, 24(2): 234-238.