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 simplif...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.展开更多
For the prediction of protein structure, we propose the solution based on parallel genetic algorithm. Thissolution has modified the existing algorithm by omitting the process of simulated annealing, while compensating...For the prediction of protein structure, we propose the solution based on parallel genetic algorithm. Thissolution has modified the existing algorithm by omitting the process of simulated annealing, while compensating thismodification by parallel programming to maintain the results quality. Experiments have demonstrated that the newsolution has higher processing speed and same results quality. This solution also underlines the necessity of introduc-ing the idea of parallel programming into the study of bioinformatics.展开更多
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)
文摘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.
文摘For the prediction of protein structure, we propose the solution based on parallel genetic algorithm. Thissolution has modified the existing algorithm by omitting the process of simulated annealing, while compensating thismodification by parallel programming to maintain the results quality. Experiments have demonstrated that the newsolution has higher processing speed and same results quality. This solution also underlines the necessity of introduc-ing the idea of parallel programming into the study of bioinformatics.
