由分子生物學的中心教條可知，蛋白質是由DNA序列轉錄成mRMA再轉譯而成的，而蛋白質的功能則必須由結構來決定，普遍的研究都是使用序列比對加入結構資訊以找出潛在功能，此法常造成不相似或演化關係較遠的序列無法找出功能所在，基於此，本篇論文中使用結構比對建立演化樹，藉由結構比對樹與序列比對樹來分析序列、結構、功能與演化之間的關係，所使用的方法首先透過CE結構比對工具對蛋白質結構進行比對，將所需的結果存成距離矩陣後，使用UPGMA演算法來對距離矩陣進行循序分群且使用演化樹來呈現，對於每個蛋白質結構，我們加入其所屬的酵素命名編號來標明它的功能。
本篇論文所使用的資料集為SCOP分類下的(β/α)8-Barrel構形，去除掉突變的蛋白質結構，且將具有多個其他Domain的PDB檔進行切割後，依SCOP的最底層分類Species分別隨機的挑出239個蛋白質結構來進行結構比對。經由結構比對樹的建立及酵素命名編號的標註後，將其與ClustalW所產生的序列比對樹做分析比較，由結果得知，不論序列間一致率的高或低，結構比對樹對於功能的分群較為一致，且可發現到在相同功能群裡存在著序列演化關係相當遠的序列，甚至可看到分屬不同的超家族卻存在於同一功能群等種種序列、結構、功能及演化關係，基於此理由，本研究建議在進行以結構為基底的序列比對時，也可使用結構比對的結果做相互的分析，藉此找出一些潛在的關係。

Central dogma of molecular biology states that DNA carries the genetic information which is transcribed to mRNA and subsequently translated to protein. And function of protein is determined from protein structure. Widespread researches all use the sequence alignment to join the structure information to find out the latent function. This method often causes not alike or relationship of evolutionary the farther sequence can't find out the function. According to this, the usage of structure alignment builds up evolutionary tree in this thesis, by the structure alignment tree and the sequence alignment tree to the relation of that analyze the sequence, structure, function and evolution. The first step of our method used carries on the alignment to the protein structure through the CE tool and will need of as a result save the distance matrix. Using the UPGMA algorithm come to carries on to the distance matrix to divide into the cluster and the usage of evolutionary tree in proper order to present. For each protein structure, we join the EC number that it belongs to mark clearly its function.
The dataset that this thesis uses is the TIM-Barrel fold under the SCOP classification. Discard the mutants and will have after many PDB files of other multi-domains carry on incising. According to the SCOP most the first floor classification Species picks 239 protein structures random respectively to carry on structure alignment. After noting through the establishment of the structure alignment tree and the mark of the EC number, will it with ClustalW produce of the sequence alignment tree does the analysis comparison. By as a result know, in spite of the sequence identity of high or low. The function cluster for structure alignment tree is more consistent and can find in same function cluster rather far sequence of existing the relation of sequence evolutionary. even can see accordingly belong to the different superfamily but exist wait for various sequence, structure function and evolution in same function cluster. According to this reason, this research suggests while carrying on taking structure as the sequence alignment of the base. Also can use the structure alignment to as a result do the mutual analysis and find out some latent relations by this.

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