Molecular docking is an important tool in screening large libraries of compounds to determine the interactions between potential drugs and the target proteins. The molec- ular docking problem is how to locate a good c...Molecular docking is an important tool in screening large libraries of compounds to determine the interactions between potential drugs and the target proteins. The molec- ular docking problem is how to locate a good conformation to dock a ligand to the large molecule. It can be formulated as a parameter optimization problem consisting of a scoring function and a global optimization method. Many docking methods have been developed with primarily these two parts varying. In this paper, a variety of particle swarm optimization （PSO） variants were introduced to cooperate with the semiempir- ical free energy force field in AutoDock 4.05. The search ability and the docking accu- racy of these methods were evaluated by multiple redocking experiments. The results demonstrate that PSOs were more suitable than Lamarckian genetic algorithm （LGA）. Among all of the PSO variants, FIPS takes precedence over others. Compared with the four state-of-art docking methods-GOLD, DOCK, FlexX and AutoDock with LGA, AutoDock cooperated with FIPS is more accurate. Thus, FIPS is an efficient PSO vari- ant which has promising prospects that can be expected in the application to virtual screening.展开更多
The most softwares for protein-protein docking are regarded as two proteins being rigid, and take no account of the flexibility of proteins, which causes conformation variety of the interface because of interaction of...The most softwares for protein-protein docking are regarded as two proteins being rigid, and take no account of the flexibility of proteins, which causes conformation variety of the interface because of interaction of the interface amino acids. On the premise of the rigidity of protein-protein docking, by the method of molecular dynamic simulation, we search the protein-protein interface conformations of the complexes which grounded on the rigid docking. Since the interaction of the amino acid was taken into account, to a certain extent, the complex conformations are more perfect.展开更多
基金This work was under Grand by the Natural Science Foundation of China （No. 60803074）, and the Fundamental Research Funds for the Central Universi- ties （No. DUT10JR06）.
文摘Molecular docking is an important tool in screening large libraries of compounds to determine the interactions between potential drugs and the target proteins. The molec- ular docking problem is how to locate a good conformation to dock a ligand to the large molecule. It can be formulated as a parameter optimization problem consisting of a scoring function and a global optimization method. Many docking methods have been developed with primarily these two parts varying. In this paper, a variety of particle swarm optimization （PSO） variants were introduced to cooperate with the semiempir- ical free energy force field in AutoDock 4.05. The search ability and the docking accu- racy of these methods were evaluated by multiple redocking experiments. The results demonstrate that PSOs were more suitable than Lamarckian genetic algorithm （LGA）. Among all of the PSO variants, FIPS takes precedence over others. Compared with the four state-of-art docking methods-GOLD, DOCK, FlexX and AutoDock with LGA, AutoDock cooperated with FIPS is more accurate. Thus, FIPS is an efficient PSO vari- ant which has promising prospects that can be expected in the application to virtual screening.
文摘The most softwares for protein-protein docking are regarded as two proteins being rigid, and take no account of the flexibility of proteins, which causes conformation variety of the interface because of interaction of the interface amino acids. On the premise of the rigidity of protein-protein docking, by the method of molecular dynamic simulation, we search the protein-protein interface conformations of the complexes which grounded on the rigid docking. Since the interaction of the amino acid was taken into account, to a certain extent, the complex conformations are more perfect.
