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CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints
Ouyang, Xuchang1; Zhou, Shuo2; Su, Chinh Tran To1; Ge, Zemei2; Li, Runtao2; Kwoh, Chee Keong1
关键词Covalent Docking Covalent Drug Molecular Docking Virtual Screening Computer-aided Drug Design
刊名JOURNAL OF COMPUTATIONAL CHEMISTRY
2013-02-05
DOI10.1002/jcc.23136
34期:4页:326-336
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Chemistry, Multidisciplinary
资助者Singapore MOE AcRF ; National Natural Science Foundation of China ; Singapore MOE AcRF ; National Natural Science Foundation of China
研究领域[WOS]Chemistry
关键词[WOS]GROWTH-FACTOR RECEPTOR ; BETA-LACTAM ANTIBIOTICS ; PROTEIN-LIGAND DOCKING ; EGFR KINASE INHIBITORS ; TYROSINE KINASE ; IRREVERSIBLE INHIBITORS ; GENETIC ALGORITHM ; SCORING FUNCTIONS ; FLEXIBLE DOCKING ; DRUG DESIGN
英文摘要

Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, partly due to the limitations of proper computational tools for covalent docking, most covalent drugs are not discovered systematically. In this article, we present a new covalent docking package, the CovalentDock, built on the top of the source code of Autodock. We developed an empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. Integrated preparation scripts are also written for the automation of the whole covalent docking workflow. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock. Experiments also suggest that CovalentDock is capable of covalent virtual screening with satisfactory enrichment performance. In addition, the investigation on the results also shows that the chirality and target selectivity along with the molecular geometry constrains are well preserved by CovalentDock, showing great capability of this method in the application for covalent drug discovery. (C) 2012 Wiley Periodicals, Inc.

语种英语
所属项目编号MOE2008-T2-1-074 ; 21172011
资助者Singapore MOE AcRF ; National Natural Science Foundation of China ; Singapore MOE AcRF ; National Natural Science Foundation of China
WOS记录号WOS:000313723500008
Citation statistics
Cited Times:49[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/400002259/53222
Collection北京大学药学院
作者单位1.Nanyang Technol Univ, Sch Comp Engn, BioInformat Res Ctr, Singapore 639798, Singapore
2.Peking Univ, Sch Pharmaceut Sci, State Key Lab Nat & Biomimet Drugs, Beijing 100191, Peoples R China
Recommended Citation
GB/T 7714
Ouyang, Xuchang,Zhou, Shuo,Su, Chinh Tran To,et al. CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY,2013,34(4):326-336.
APA Ouyang, Xuchang,Zhou, Shuo,Su, Chinh Tran To,Ge, Zemei,Li, Runtao,&Kwoh, Chee Keong.(2013).CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints.JOURNAL OF COMPUTATIONAL CHEMISTRY,34(4),326-336.
MLA Ouyang, Xuchang,et al."CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints".JOURNAL OF COMPUTATIONAL CHEMISTRY 34.4(2013):326-336.
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