Protein-Protein Interface Analysis and Hot Spots Identification for Chemical Ligand Design

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	Protein-Protein Interface Analysis and Hot Spots Identification for Chemical Ligand Design
	Chen, Jing 1,2,3; Ma, Xiaomin 1,2,3; Yuan, Yaxia 1,2,3; Pei, Jianfeng 3; Lai, Luhua 1,2,3
刊名	CURRENT PHARMACEUTICAL DESIGN
	2014-03-01
卷号	20 期号:8 页码:1192-1200
关键词	Protein-protein Interface Analysis Small Molecular Binder Binding Site Detection Ligandability Hot Spots Pocket V.3
ISSN号	1381-6128
英文摘要	Rational design for chemical compounds targeting protein-protein interactions has grown from a dream to reality after a decade of efforts. There are an increasing number of successful examples, though major challenges remain in the field. In this paper, we will first give a brief review of the available methods that can be used to analyze protein-protein interface and predict hot spots for chemical ligand design. New developments of binding sites detection, ligandability and hot spots prediction from the author's group will also be described. Pocket V.3 is an improved program for identifying hot spots in protein-protein interface using only an apo protein structure. It has been developed based on Pocket V.2 that can derive receptor-based pharmacophore model for ligand binding cavity. Given similarities and differences between the essence of pharmacophore and hot spots for guiding design of chemical compounds, not only energetic but also spatial properties of protein-protein interface are used in Pocket V.3 for dealing with protein-protein interface. In order to illustrate the capability of Pocket V.3, two datasets have been used. One is taken from ASEdb and BID having experimental alanine scanning results for testing hot spots prediction. The other is taken from the 2P2I database containing complex structures of protein-ligand binding at the original protein-protein interface for testing hot spots application in ligand design.
语种	英语
出版者	BENTHAM SCIENCE PUBL LTD
WOS记录号	WOS:000334309400004
内容类型	期刊论文
源URL	[http://ir.iccas.ac.cn/handle/121111/51953]
专题	中国科学院化学研究所
通讯作者	Lai, Luhua
作者单位	1.Peking Univ, Coll Chem & Mol Engn, BNLMS, State Key Lab Struct Chem Unstable & Stable Speci, Beijing 100871, Peoples R China 2.Peking Univ, Coll Chem & Mol Engn, Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China 3.Peking Univ, Ctr Quantitat Biol, Beijing 100871, Peoples R China
推荐引用方式 GB/T 7714	Chen, Jing,Ma, Xiaomin,Yuan, Yaxia,et al. Protein-Protein Interface Analysis and Hot Spots Identification for Chemical Ligand Design[J]. CURRENT PHARMACEUTICAL DESIGN,2014,20(8):1192-1200.
APA	Chen, Jing,Ma, Xiaomin,Yuan, Yaxia,Pei, Jianfeng,&Lai, Luhua.(2014).Protein-Protein Interface Analysis and Hot Spots Identification for Chemical Ligand Design.CURRENT PHARMACEUTICAL DESIGN,20(8),1192-1200.
MLA	Chen, Jing,et al."Protein-Protein Interface Analysis and Hot Spots Identification for Chemical Ligand Design".CURRENT PHARMACEUTICAL DESIGN 20.8(2014):1192-1200.