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D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics

文献类型：期刊论文

作者Chen, Zhaoqiang2,3; Zhang, Xinben2; Peng, Cheng2,3; Wang, Jinan2; Xu, Zhijian2,3; Chen, Kaixian1,2,3; Shi, Jiye4; Zhu, Weiliang1,2,3
刊名JOURNAL OF CHEMICAL INFORMATION AND MODELING
出版日期2019-08-01
卷号59期号:8页码:3353-3358
ISSN号1549-9596
DOI10.1021/acs.jcim.9b00332
通讯作者Xu, Zhijian(zjxu@simma.ac.cn) ; Shi, Jiye(Jiye.Shi@ucb.com) ; Zhu, Weiliang(wlzhu@simm.ac.cn)
英文摘要The intrinsic dynamic properties of the ligand-binding pockets of proteins are important for the protein function mechanism and thus are useful to drug discovery and development. Few methods are available to study the dynamic properties, such as pocket stability, continuity, and correlation. In this work, we develop a method and web server, namely, D3Pockets, for exploring the dynamic properties of the protein pocket based on either molecular dynamics (MD) simulation trajectories or conformational ensembles. Application of D3Pockets on five target proteins as examples, namely, HIV-1 protease, BACE1, L-ABP, GPX4, and GR, uncovers more information on the dynamic properties of the ligand-binding pockets, which should be helpful to understanding protein function mechanism and drug design.
WOS关键词LIGAND-BINDING-SITES ; DRUG ; DRUGGABILITY ; CAVITIES ; PREDICTION ; SURFACES ; IDENTIFICATION ; ALGORITHM ; DISCOVERY ; GEOMETRY
资助项目National Key Research and Development Program[2016YFA0502301] ; National Natural Science Foundation of China[81573350] ; National Natural Science Foundation of China[81872797] ; National Science & Technology Major Project Key New Drug Creation and Manufacturing Program, China[2018ZX09711002] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (second phase)[nsfc2015_447]
WOS研究方向Pharmacology & Pharmacy ; Chemistry ; Computer Science
语种英语
WOS记录号WOS:000483436400001
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.183/handle/2S10ELR8/288648]  
专题中国科学院上海药物研究所
通讯作者Xu, Zhijian; Shi, Jiye; Zhu, Weiliang
作者单位1.Pilot Natl Lab Marine Sci & Technol Qingdao, Open Studio Druggabil Res Marine Nat Prod, 1 Wenhai Rd, Qingdao 266237, Shandong, Peoples R China
2.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, CAS Key Lab Receptor Res, Shanghai 201203, Peoples R China
3.Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China
4.UCB Biopharma SPRL, Chemin Foriest, B-1420 Braine I Alleud, Belgium
推荐引用方式
GB/T 7714		 Chen, Zhaoqiang,Zhang, Xinben,Peng, Cheng,et al. D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2019,59(8):3353-3358.
APA Chen, Zhaoqiang.,Zhang, Xinben.,Peng, Cheng.,Wang, Jinan.,Xu, Zhijian.,...&Zhu, Weiliang.(2019).D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics.JOURNAL OF CHEMICAL INFORMATION AND MODELING,59(8),3353-3358.
MLA Chen, Zhaoqiang,et al."D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics".JOURNAL OF CHEMICAL INFORMATION AND MODELING 59.8(2019):3353-3358.

入库方式： OAI收割

来源：上海药物研究所

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