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Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action
Yang, XH; Liu, HH; Liu, JB; Li, F; Li, XH; Shi, LL; Chen, JW; Liu, JB (reprint author), Minist Environm Protect, Nanjing Inst Environm Sci, 8 Jiangwangmiao Steet, Nanjing 210042, Jiangsu, Peoples R China.; Chen, JW (reprint author), Dalian Univ Technol, Sch Environm Sci & Technol, Linggong Rd 2, Dalian 116024, Peoples R China. Email:ljn@nies.org; jwchen@dlut.edu.cn
Source PublicationCHEMICAL RESEARCH IN TOXICOLOGY
ISSN0893-228X
2016-09-01
Volume29Issue:9Pages:1565-1570
DOI10.1021/acs.chemrestox.6b00245
Contribution Rank[Yang, Xianhai; Liu, Jining; Shi, Lili] Minist Environm Protect, Nanjing Inst Environm Sci, 8 Jiangwangmiao Steet, Nanjing 210042, Jiangsu, Peoples R China; [Liu, Huihui] Nanjing Univ Sci & Technol, Sch Environm & Biol Engn, Jiangsu Key Lab Chem Pollut Control & Resources R, Nanjing 210094, Jiangsu, Peoples R China; [Li, Fei] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China; [Li, Xuehua; Chen, Jingwen] Dalian Univ Technol, Sch Environm Sci & Technol, Minist Educ, Key Lab Ind Ecol & Environm Engn, Dalian 116024, Peoples R China
Department中科院海岸带环境过程与生态修复重点实验室
AbstractMolecular modeling has become an essential tool in predicting and simulating endocrine disrupting effects of chemicals. A key prerequisite for successful application of molecular modeling lies in the correctness of 3D structure for biomacromolecules to be simulated. To date, there are several databases that can provide the experimentally determined 3D structures. However, commonly, there are many challenges or disadvantageous factors, e.g., (a) lots of 3D structures for a given biomacromolecular target in the protein database; (b) the quality variability for those structures; (c) belonging to different species; (d) mutant amino acid residue in key positions, and so on. Once an inappropriate 3D structure of a target biomacromolecule was selected in molecular modeling, the accuracy and scientific nature of the modeling results could be inevitably affected. In this article, based on literature survey and an analysis of the 3D structure characterization of biomacromolecular targets belonging to the endocrine system in protein databases, six principles were proposed to guide the selection of the appropriate 3D structure of biomacromolecules. The principles include considering the species diversity, the mechanism of action, whether there are mutant amino acid residues, whether the number of protein chains is correct, the degree of structural similarity between the ligand in 3D structure and the target compounds, and other factors, e.g., the experimental pH conditions of the structure, determined process and resolution.
SubtypeArticle
Indexed BySCI
Language英语
WOS KeywordPOLYBROMINATED DIPHENYL ETHERS ; THYROID-HORMONE-BINDING ; HUMAN SERUM-ALBUMIN ; IN-VITRO ; ESTROGEN-RECEPTOR ; RISK-ASSESSMENT ; RECOMBINANT TRANSTHYRETIN ; SCIENTIFIC STATEMENT ; EVOLUTIONARY CHANGES ; CHEMICALS
WOS Research AreaPharmacology & Pharmacy ; Chemistry ; Toxicology
WOS IDWOS:000383733300021
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.yic.ac.cn/handle/133337/17201
Collection中科院海岸带环境过程与生态修复重点实验室
Corresponding AuthorLiu, JB (reprint author), Minist Environm Protect, Nanjing Inst Environm Sci, 8 Jiangwangmiao Steet, Nanjing 210042, Jiangsu, Peoples R China.; Chen, JW (reprint author), Dalian Univ Technol, Sch Environm Sci & Technol, Linggong Rd 2, Dalian 116024, Peoples R China. Email:ljn@nies.org; jwchen@dlut.edu.cn
Recommended Citation
GB/T 7714
Yang, XH,Liu, HH,Liu, JB,et al. Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action[J]. CHEMICAL RESEARCH IN TOXICOLOGY,2016,29(9):1565-1570.
APA Yang, XH.,Liu, HH.,Liu, JB.,Li, F.,Li, XH.,...&jwchen@dlut.edu.cn.(2016).Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action.CHEMICAL RESEARCH IN TOXICOLOGY,29(9),1565-1570.
MLA Yang, XH,et al."Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action".CHEMICAL RESEARCH IN TOXICOLOGY 29.9(2016):1565-1570.
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