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研究生: 曾彥皆
Tseng, yen-jie
論文名稱: 廣泛搜尋有機小分子代謝和結合的工具
A comprehensive web tool for searching metabolic and binding data for small organic molecules
指導教授: 林志侯
Lin, Thy-Hou
口試委員: 莊永仁
Chuang, Yung-Jen
楊立威
Yang, Lee-Wei
學位類別: 碩士
Master
系所名稱: 生命科學暨醫學院 - 分子醫學研究所
Institute of Molecular Medicine
論文出版年: 2012
畢業學年度: 101
語文別: 中文
論文頁數: 54
中文關鍵詞: 藥物工作
外文關鍵詞: Drug, tool
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  • 在基礎生物醫學研究中由於化合物能夠成為藥物的可能性很低,因此透過高通量的方式快速大量篩檢大量的化合物以縮短研發的時間降低成本,在過去的時代裡有許多化合物與蛋白做過無數的研究以及探討,能夠完善的使用這些資訊對於使用者將省下許多實驗的時間以及成本,因此建立一個完善的資料庫是重要的是必須的(An, Bartels, & Vodovotz, 2011)。
    Comprehemsive Compound Bank(CCB) 是一個以化合物為主的資料庫、化學與醫學相關的資料庫,收集詳細的配體和一般蛋白或酵素在體內的資訊。該資料庫以PubChem的化合物為基礎,相似度找出一群相似的化學結構後再與其他蒐集來的資料進行比對。資料庫資料包括蒐集包括KEGG的千筆資料、DrugBank的千筆資料、BindingDB的萬筆資訊。CCB以化合物為主連接其他蒐集來的資訊,這些蒐集來的資訊皆以化合物為主包括化合物的基本簡介、化合物對蛋白質的實驗數據、化合物在生物體內進行的化學反應。許多的數據也連接於各大資料庫包括PubChem、KEGG、BindingDB、DrugBank、UniProKB等各大資料庫。CCB應用於藥物標把的研究、藥物設計、藥物對接、藥物篩選、藥物代謝的預測、藥物相互作用的預測。CCB另一項功能是將常見的化學結構格式轉換成不常使用的化學格式對於有特殊需求的使用者而言這是一項便利以及新奇、獨特的功能。CCB輸入化學結構的方式包括透過圖形化的網頁介面進行檔案轉換與搜尋功能提供了更多元的選擇讓使用者能夠更便利的使用。


    Due to the low probabilities of compounds becoming medicines, high throughput drug screening is applied in a basic biomedical research center to fast screen mass compounds to reduce research time and cost.Since there were numerous studies on and investigations into many compounds and proteins, it will save a lot of drug researchers' time and cost if the information could be well utilized. Thus, establishing a thorough database is vitally essential.
    Comprehensive Compound Bank (CCB) is a special biological and chemical information database that details reactions and combinations of ligands on protein in a body. With similarity comparisons of compound bases in PubChem, the database looks for similar chemical structures and combines them with other collected data.
    Information in CCB includes 1,000 KEGG data, 1,000 Drug Bank data and 10,000 BindingDB data.Mainly based on compounds, CCB links information otherwise collected, including basic introduction of compounds, experiment data of compounds on proteins, chemical reactions of compounds undergoing in a biological organism.
    Many data are also linked to various major databases such as PubChem, KEGG, BindingDB, DrugBank, and UniProKB.CCB is applied to research on drug targets, drug design, drug docking, drug screening and on predictions of drug metabolism and interaction. Another function of CCB is to transform commonly-seen chemical structures into infrequently-used chemical formats – a convenient, novel, unique function for drug researchers with special requests.Methods to input chemical structures into CCB, through graphic interfaces, include file transformation and search function, providing diverse options of greater convenience for drug researchers.

    Content 2 List of figures 3 List of tabl 4 摘要 5 Abstract 6 第1章節-簡介 7 1-1 背景 7 1-2 動機與目標 7 第2章節-材料與方法 9 2-1 資料來源 9 2-1-1 KEGG(Kyoto Encyclopedia of Genes and Genomes) 9 2-1-2 PubChem 9 2-1-3 DrugBank 10 2-1-4 BindingDB 11 2-2 電腦工具 12 2-2-1 Linux 12 2-2-2 Open Babel 12 2-2-3JME 13 2-3 CCB 的架構 14 2-4 CCB的建置內容 16 2-5 CCB的網頁建構 17 2-6 CCB的更新 18 第3章節-結果 19 3-1 CCB的資料組成 19 3-2-1 CCB介紹 19 3-2-2 CCB 轉換格式 19 3-2-3 CCB 相似度搜尋 20 第4章節-討論 21 第5章節-文獻 45 第6章節-附錄 47

    An, G., Bartels, J., & Vodovotz, Y. (2011). In Silico Augmentation of the Drug Development Pipeline: Examples from the study of Acute Inflammation. Drug Dev Res, 72(2), 187-200. doi: 10.1002/ddr.20415
    Chen, Bin. (2009). PubChem as a Source of Polypharmacology. J. Chem. Inf. Model.
    Chen, Xi. (2001). <The Binding Database Data Management and Interface Design Bioinformatics.pdf>. bioinformatics.
    Filimonov, Dmitrii. (1998). Chemical Similarity Assessment through Multilevel Neighborhoods of Atoms  Definition and Comparison with the Other Descriptors. J. Chem. Inf. Comput. Sci.
    goto, susumu. (1998). LIGAND chemical database for enzyme reactions. bioinformatics.
    Goto, Susumu. (2002). database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404 (2002). Nucleic Acids Research.
    Han, L. (2010). The Text-mining based PubChem Bioassay neighboring analysis. BMC Bioinformatics, 11, 549. doi: 10.1186/1471-2105-11-549
    Ihlenfeldt, W. D. (2009). The PubChem chemical structure sketcher. J Cheminform, 1(1), 20. doi: 10.1186/1758-2946-1-20
    Kanehisa, Minoru. (1997). A database for post-genome analysis. Trends in Genetics, 13(9), 375-376. doi: 10.1016/s0168-9525(97)01223-7
    Knox, C. (2011). DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res, 39(Database issue), D1035-1041. doi: 10.1093/nar/gkq1126
    Li, Q. (2009). A novel method for mining highly imbalanced high-throughput screening data in PubChem. Bioinformatics, 25(24), 3310-3316. doi: 10.1093/bioinformatics/btp589
    Liu, T. (2007). BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res, 35(Database issue), D198-201. doi: 10.1093/nar/gkl999
    O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. J Cheminform, 3, 33. doi: 10.1186/1758-2946-3-33
    Rohrer, Sebastian G. (2009). Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data. J. Chem. Inf. Model.
    Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., . . . Hassanali, M. (2008). DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res, 36(Database issue), D901-906. doi: 10.1093/nar/gkm958
    Wishart, D. S., Knox, C., Guo, A. C., Shrivastava, S., Hassanali, M., Stothard, P., . . . Woolsey, J. (2006). DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res, 34(Database issue), D668-672. doi: 10.1093/nar/gkj067
    Xie, X. Q. (2010). Exploiting PubChem for Virtual Screening. Expert Opin Drug Discov, 5(12), 1205-1220. doi: 10.1517/17460441.2010.524924

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