代謝體學是專門研究在代謝路徑中小分子代謝物的生產率和量化的過程。代謝體可被定義為在一個特定的細胞、器官或有機體中小分子代謝物的完整反應關係。因為它獨特的聚焦在小分子和小分子之間的交互作用，因此我們發現代謝體學被廣泛應用在藥物的發現、藥物的評定、臨床毒物學、臨床化學、功能基因體學和營養基因體學。
本研究是從KEGG資料庫的KEGG REACTION下載資料，找出和一個小分子化合物反應的所有酵素，再利用BRENDA資料庫找出酵素的序列，並且利用ClustalW做多序列排比，將排比好的酵素序列依照胺基酸的酸鹼值、凡德瓦體積、表面積、疏水性等四個物理化學性質編碼，利用編碼得到的矩陣，我們找出所有序列間物理化學性質最相似之片段，希望研究得到的結果能尋找現有藥物的可能目標蛋白質和可治療何種疾病。

Metabolomics is a newly emerging field of ‘omics’ research concerned with the high-throughput identification and quantification of the small molecule metabolites in the metabolome. The metabolome can be defined as the complete complement of all small molecule metabolites found in a specific cell, organ or organism.
Because of its unique focus on the interactions between small molecules, metabolomics is finding widespread applications in drug discovery , drug assessment , clinical toxicology , clinical chemistry and nutritional genomics.
Our research begins with downloading the data from the KEGG REACTION database. We find that certain ligand can have interaction with some enzymes. We search for all the sequences of the enzymes from the BRENDA database then use the program ClustalW to proceed multiple sequence alignment. There are four physicochemical quantities about amino acid. They are acidity, Van der waal volume, surface area and hydrophobicity. According to the four physicochemical quantities of amino acid, we can find four matrixes. With the four matrixes, we can get the most similar area in the sequences. It may be useful in drug discovery and drug design.

摘要 I
Abstract II
誌謝 III
表目錄 IV
圖目錄 V
第一章 緒論 1
計算代謝體學現行的發展 1
(一)代謝體學的定義 1
(二) 代謝體學資料庫 2
(三) 代謝體學資料庫管理系統和資料規格化 5
(四) 代謝體學的光譜分析工具 9
(五) 光譜分析-化學計量法和代謝體學資料分析 10
(六) 光譜分析-標定代謝成分 11
(七) 代謝的模型化和代謝體學數據的解釋 12
(八) 未來的趨勢 15
第二章 研究背景與研究動機 16
一. 酵素 16
(一) 酵素的分類 16
(二) 系統命名法 16
二. 蛋白質功能性區域概論 17
三. 功能區資料庫 20
四. 未來的發展 22
五. 研究動機 23
第三章 研究材料與研究方法 25
一. KEGG資料庫 25
(一) KEGG資料庫的源起 25
(二) KEGG資料庫的資源 26
二.多序列排比軟體工具-ClustalW 33
三.研究流程 36
(一)取得KEGG的資料 37
(二) 彙整資料 39
(三) 尋找序列並做多序列排比 40
(四) 利用物理化學性質編碼 41
(五) 計算蛋白質序列中物理化學特性的相似度 41
第四章 結果與討論 44
一.尋找序列間物理化學性質最相似的片段 44
二.討論 90
(一) 尋找蛋白質序列物理化學性質的相似性 90
(二) 製做演化樹 90
(三) Acylcarnitine 90
(四) Adenylic acid 90
第五章 結論 91
參考文獻 92
附錄、與基質化合物起反應之酵素列表 94

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