PSI-DOCK: Towards highly efficient and accurate flexible ligand docking

doi:10.1002/prot.20790

CORC > 北京大学 > 化学与分子工程学院

	PSI-DOCK: Towards highly efficient and accurate flexible ligand docking
	Pei, JF ; Wang, Q ; Liu, ZM ; Li, QL ; Yang, K ; Lai, LH
刊名	proteins structure function and bioinformatics
	2006
关键词	scoring docking SCORE 3.0 PSI-DOCK drug design message passing interface (MPI) virtual screening INCREMENTAL CONSTRUCTION ALGORITHM BINDING FREE-ENERGY GENETIC ALGORITHM MOLECULAR DOCKING AUTOMATED DOCKING TABU SEARCH PROTEIN AFFINITY VALIDATION INHIBITORS
DOI	10.1002/prot.20790
英文摘要	We have developed a new docking method, Pose-Sensitive Inclined (PSI)-DOCK, for flexible ligand docking. An improved SCORE function has been developed and used in PSI-DOCK for binding free energy evaluation. The improved SCORE function was able to reproduce the absolute binding free energies of a training set of 200 protein-ligand complexes with a correlation coefficient of 0.788 and a standard error of 8.13 kJ/mol. For ligand binding pose exploration, a unique searching strategy was designed in PSI-DOCK. In the first step, a tabu-enhanced genetic algorithm with a rapid shape-complementary scoring function is used to roughly explore and store potential binding poses of the ligand. Then, these predicted binding poses are optimized and compete against each other by using a genetic algorithm with the accurate SCORE function to determine the binding pose with the lowest docking energy. The PSI-DOCK 1.0 program is highly efficient in identifying the experimental binding pose. For a test dataset of 194 complexes, PSI-DOCK 1.0 achieved a 67% success rate (RMSD < 2.0 angstrom) for only one run and a 74% success rate for 10 runs. PSI-DOCK can also predict the docking binding free energy with high accuracy. For a test set of 64 complexes, the correlation between the experimentally observed binding free energies and the docking binding free energies for 64 complexes is r = 0.777 with a standard deviation of 7.96 kJ/mol. Moreover, compared with other docking methods, PSI-DOCK 1.0 is extremely easy to use and requires minimum docking preparations. There is no requirement for the users to add hydrogen atoms to proteins because all protein hydrogen atoms and the flexibility of the terminal protein atoms are intrinsically taken into account in PSI-DOCK. There is also no requirement for the users to calculate partial atomic charges because PSI-DOCK does not calculate an electrostatic energy term. These features are not only convenient for the users but also help to avoid the influence of different preparation methods.; Biochemistry & Molecular Biology; Biophysics; SCI(E); PubMed; 25; ARTICLE; 4; 934-946; 62
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/199409]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Pei, JF,Wang, Q,Liu, ZM,et al. PSI-DOCK: Towards highly efficient and accurate flexible ligand docking[J]. proteins structure function and bioinformatics,2006.
APA	Pei, JF,Wang, Q,Liu, ZM,Li, QL,Yang, K,&Lai, LH.(2006).PSI-DOCK: Towards highly efficient and accurate flexible ligand docking.proteins structure function and bioinformatics.
MLA	Pei, JF,et al."PSI-DOCK: Towards highly efficient and accurate flexible ligand docking".proteins structure function and bioinformatics (2006).