A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

doi:10.1007/s00894-013-2005-7

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	A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions
	Liu, Yingtao; Xu, Zhijian; Yang, Zhuo; Chen, Kaixian; Zhu, Weiliang
刊名	JOURNAL OF MOLECULAR MODELING
	2013-11
卷号	19 期号:11 页码:5015-5030
关键词	Halogen bonding Knowledge-based scoring function Potential of mean forces Protein-ligand interaction sigma-hole
ISSN号	1610-2940
DOI	10.1007/s00894-013-2005-7
文献子类	Article
英文摘要	Halogen bonding, a non-covalent interaction between the halogen sigma-hole and Lewis bases, could not be properly characterized by majority of current scoring functions. In this study, a knowledge-based halogen bonding scoring function, termed XBPMF, was developed by an iterative method for predicting protein-ligand interactions. Three sets of pairwise potentials were derived from two training sets of protein-ligand complexes from the Protein Data Bank. It was found that two-dimensional pairwise potentials could characterize appropriately the distance and angle profiles of halogen bonding, which is superior to one-dimensional pairwise potentials. With comparison to six widely used scoring functions, XBPMF was evaluated to have moderate power for predicting protein-ligand interactions in terms of "docking power", "ranking power" and "scoring power". Especially, it has a rather satisfactory performance for the systems with typical halogen bonds. To the best of our knowledge, XBPMF is the first halogen bonding scoring function that is not dependent on any dummy atom, and is practical for high-throughput virtual screening. Therefore, this scoring function should be useful for the study and application of halogen bonding interactions like molecular docking and lead optimization.
资助项目	National Natural Science Foundation of China[81273435] ; National Natural Science Foundation of China[21021063] ; National Natural Science Foundation of China[91013008] ; State Key Laboratory of Drug Research[SIMM1203KF-01]
WOS关键词	MECHANICAL METHOD PM6-DH2X ; RATIONAL DRUG DESIGN ; BINDING AFFINITIES ; FORCE-FIELD ; MOLECULAR DOCKING ; SIGMA-HOLE ; GENETIC ALGORITHM ; ACCURATE DOCKING ; PDBBIND DATABASE ; COMPLEXES
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science
语种	英语
出版者	SPRINGER
WOS记录号	WOS:000326193200040
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/277406]
专题	药物发现与设计中心
通讯作者	Zhu, Weiliang
作者单位	Chinese Acad Sci, Shanghai Inst Mat Med, CAS Key Lab Receptor Struct & Funct, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China
推荐引用方式 GB/T 7714	Liu, Yingtao,Xu, Zhijian,Yang, Zhuo,et al. A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions[J]. JOURNAL OF MOLECULAR MODELING,2013,19(11):5015-5030.
APA	Liu, Yingtao,Xu, Zhijian,Yang, Zhuo,Chen, Kaixian,&Zhu, Weiliang.(2013).A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions.JOURNAL OF MOLECULAR MODELING,19(11),5015-5030.
MLA	Liu, Yingtao,et al."A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions".JOURNAL OF MOLECULAR MODELING 19.11(2013):5015-5030.