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Homology Modeling and Structure Validation of the Adenosine A(1) Receptor
Ke Yan-Rong; Jin Hong-Wei; Liu Zhen-Ming; Zhang Liang-Ren
关键词Molecular dynamics simulation Adenosine A(1) receptor Homology modeling GOLD Virtual screening
刊名ACTA PHYSICO-CHIMICA SINICA
2010-10-01
DOI10.3866/PKU.WHXB20100916
26期:10页:2833-2839
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Chemistry, Physical
资助者National S&amp ; T Major Project Foundation, China ; National S&amp ; T Major Project Foundation, China
研究领域[WOS]Chemistry
关键词[WOS]SITE-DIRECTED MUTAGENESIS ; MOLECULAR-DYNAMICS ; BINDING-SITE ; CRYSTAL-STRUCTURE ; LIGAND-BINDING ; DOCKING ; ANTAGONIST ; SELECTIVITY
英文摘要

A three dimensional structure model of the adenosine A(1) receptor was built using homology modeling. The antagonist DPCPX was docked into the model protein to form a receptor-ligand complex. A molecular dynamics simulation over 5 ns was performed for this complex. We selected 12 protein structures, including the average structure obtained from the last 2 ns of the simulation and 11 frames extracted after equilibration for the study. A database comprising 52 active antagonists and 1000 decoys was then docked into the 12 protein models using DOCK, VINA, and GOLD software packages and these molecules were ranked by their docking scores. The best model protein with the highest enrichment factor (EF) and the largest area under the ROC (AU-ROC) was chosen for further study. The results from the enrichment factor at 10% of the ranked database (EF10) and AU-ROC calculations indicate that GOLD is the best virtual screening software for the adenosine A1 receptor. GOLD docking results suggest that optimized adenosine A(1) receptor protein structures, Favg and F5, can be used for virtual screening and for novel design to discover more potent antagonists.

语种中文
所属项目编号2009ZX09501-002
资助者National S&amp ; T Major Project Foundation, China ; National S&amp ; T Major Project Foundation, China
WOS记录号WOS:000282220200037
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/59220
Collection北京大学药学院
作者单位Peking Univ, Hlth Sci Ctr, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing 100191, Peoples R China
Recommended Citation
GB/T 7714
Ke Yan-Rong,Jin Hong-Wei,Liu Zhen-Ming,et al. Homology Modeling and Structure Validation of the Adenosine A(1) Receptor[J]. ACTA PHYSICO-CHIMICA SINICA,2010,26(10):2833-2839.
APA Ke Yan-Rong,Jin Hong-Wei,Liu Zhen-Ming,&Zhang Liang-Ren.(2010).Homology Modeling and Structure Validation of the Adenosine A(1) Receptor.ACTA PHYSICO-CHIMICA SINICA,26(10),2833-2839.
MLA Ke Yan-Rong,et al."Homology Modeling and Structure Validation of the Adenosine A(1) Receptor".ACTA PHYSICO-CHIMICA SINICA 26.10(2010):2833-2839.
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