A fast protein-ligand docking algorithm based on hydrogen bond matching   and surface shape complementarity

doi:10.1007/s00894-009-0598-7

CORC > 北京大学 > 化学与分子工程学院

	A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity
	Luo, Wenjia ; Pei, Jianfeng ; Zhu, Yushan
刊名	journal of molecular modeling
	2010
关键词	Combinatorial optimization Docking Hydrogen bond matching Virtual screening INCREMENTAL CONSTRUCTION ALGORITHM MOLECULAR DOCKING BINDING-AFFINITY FLEXIBLE DOCKING GENETIC ALGORITHM AUTOMATED DOCKING SCORING FUNCTIONS DESIGN SEARCH VALIDATION
DOI	10.1007/s00894-009-0598-7
英文摘要	With the rapid development of structural determination of target proteins for human diseases, high throughout virtual screening based drug discovery is gaining popularity gradually. In this paper, a fast docking algorithm (H-DOCK) based on hydrogen bond matching and surface shape complementarity was developed. In H-DOCK, firstly a divide-and-conquer strategy based enumeration approach is applied to rank the intermolecular modes between protein and ligand by maximizing their hydrogen bonds matching, then each docked conformation of the ligand is calculated according to the matched hydrogen bonding geometry, finally a simple but effective scoring function reflecting mainly the van der Waals interaction is used to evaluate the docked conformations of the ligand. H-DOCK is tested for rigid ligand docking and flexible one, the latter is implemented by repeating rigid docking for multiple conformations of a small molecule and ranking all together. For rigid ligands, H-DOCK was tested on a set of 271 complexes where there is at least one intermolecular hydrogen bond, and H-DOCK achieved success rate (RMSD < 2.0 ) of 91.1%. For flexible ligands, H-DOCK was tested on another set of 93 complexes, where each case was a conformation ensemble containing native ligand conformation as well as 100 decoy ones generated by AutoDock [1], and the success rate reached 81.7%. The high success rate of H-DOCK indicates that the hydrogen bonding and steric hindrance can grasp the key interaction between protein and ligand. H-DOCK is quite efficient compared with the conventional docking algorithms, and it takes only about 0.14 seconds for a rigid ligand docking and about 8.25 seconds for a flexible one on average. According to the preliminary docking results, it implies that H-DOCK can be potentially used for large scale virtual screening as a pre-filter for a more accurate but less efficient docking algorithm.; Biochemistry & Molecular Biology; Biophysics; Chemistry, Multidisciplinary; Computer Science, Interdisciplinary Applications; SCI(E); 11; ARTICLE; 5; 903-913; 16
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/244572]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Luo, Wenjia,Pei, Jianfeng,Zhu, Yushan. A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity[J]. journal of molecular modeling,2010.
APA	Luo, Wenjia,Pei, Jianfeng,&Zhu, Yushan.(2010).A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity.journal of molecular modeling.
MLA	Luo, Wenjia,et al."A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity".journal of molecular modeling (2010).