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题名: Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening
作者: Du, HY; Brender, JR; Zhang, J; Zhang, Y
收录类别: SCIE ; PubMed ; MEDLINE
出版日期: 2015
刊名: METHODS
卷号: 71, 页码:77-84
出版者: ELSEVIER
出版地: SAN DIEGO
英文摘要: Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (<30% sequence identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures. (C) 2014 Elsevier Inc. All rights reserved.
关键词: Virtual screening ; Enrichment rate ; Ligand docking ; Protein structure prediction
作者部门: [Du, Hongying ; Brender, Jeffrey R. ; Zhang, Jian ; Zhang, Yang] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA ; [Du, Hongying] Lanzhou Univ, Dept Publ Hlth, Lanzhou 730000, Peoples R China
通讯作者: Zhang, Y (reprint author), Univ Michigan, Dept Computat Med & Bioinformat, 100 Washtenaw Ave, Ann Arbor, MI 48109 USA.
学科分类: Biochemistry & Molecular Biology
文章类型: Article
所属项目编号: National Institute of General Medical Sciences [GM083107, GM084222]
语种: 英语
DOI: 10.1016/j.ymeth.2014.08.017
ISSN号: 1046-2023
WOS记录号: WOS:000348264200011
PM记录号: 25220914
第一机构:
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内容类型: 期刊论文
URI标识: http://ir.lzu.edu.cn/handle/262010/121826
Appears in Collections:公共卫生学院_期刊论文

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Recommended Citation:
Du, HY,Brender, JR,Zhang, J,et al. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening[J]. METHODS,2015,71:77-84.
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