A Case Study of 3D Protein Structure Prediction with Genetic Algorithm and Tabu Search  

作　　者：WANG Ting1,2, ZHANG Xiaolong1, 3 1. School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China 2. College of Mobile Telecommunications, Chongqing University of Posts and Telecommunications, Chongqing 400065, China 3. State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China 

出　　处：《Wuhan University Journal of Natural Sciences》2011年第2期125-129,共5页武汉大学学报（自然科学英文版）

基　　金：Supported by the National Natural Science Foundation of China (60975031);the Scientific Research Foundation for the Returned Overseas Chinese Scholars of Ministry of Education of China, the Open Foundation of State Key Laboratory of Bioelectronics of Southeast University, China, and the Natural Science Foundation of Hubei Province, China (2008CDB344 and 2009CDA034)

摘　　要：This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplified model of protein structure. The lowest-energy values required for forming the native conformation of proteins are searched by GATS, and then the coarse structures （i.e., simplified structure） of the proteins are obtained according to the multiple angle parameters corresponding to the lowest energies. All the coarse structures form single hydrophobic cores surrounded by hydrophilic residues, which stay on the right side of the actual characteristic of protein structure. It demonstrates that this approach can predict the 3D protein structure effectively.This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplified model of protein structure. The lowest-energy values required for forming the native conformation of proteins are searched by GATS, and then the coarse structures （i.e., simplified structure） of the proteins are obtained according to the multiple angle parameters corresponding to the lowest energies. All the coarse structures form single hydrophobic cores surrounded by hydrophilic residues, which stay on the right side of the actual characteristic of protein structure. It demonstrates that this approach can predict the 3D protein structure effectively.

关 键 词：3D protein structure off-lattice AB model genetic algorithm and tabu search （GATS） 

分 类 号：O242.28[理学—计算数学] Q71[理学—数学]