Quasi-physical Algorithm for Protein Folding in an Off-Lattice Model |
| |
Authors: | LÜ Zhi-Peng HUANG Wen-Qi SHI He |
| |
Affiliation: | 1. School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;2. Academy of Mathematics and Systems Sciences, the ChineseAcademy of Sciences, Beijing 100080, China |
| |
Abstract: | 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. |
| |
Keywords: | quasi-physical algorithm conjugate gradient method protein folding off-lattice model |
本文献已被 维普 万方数据 等数据库收录! |
| 点击此处可从《理论物理通讯》浏览原始摘要信息 |
|
点击此处可从《理论物理通讯》下载全文 |
|