摘要
蛋白質的生理功能由其立體分子結構來決定。因此蛋白質結構的分析在現代生物學的研究中扮演重要的角色。結構比對可以用來比較和尋找相似的蛋白質結構，是一功能強大的工具。基於不同需求考量以及實作方法，許多蛋白質結構比對的演算法被開發出來，並已廣泛應用在蛋白質結構的分析上。其中名為SARST的蛋白質結構比對演算法，以經過特殊轉換後的蛋白質Ramachandran圖之序列資料，進行序列比對的方式來進行蛋白質結構比對。SARST具有能在一大型蛋白質結構資料庫中快速搜尋和比對的功能。
在本論文中，我們實作了SARST演算法，並加入許多改良使之成為更具應用價值的軟體工具，而且可以在網際網路上使用。並以一些來自於PDB資料庫的真實蛋白質結構資料作為樣本來測試SARST，還有一些關於SARST參數的分析比較。雖然SARST有時未必能提供更佳的一對一結構比對品質，但是它能提供極為快速的一對全部的相似蛋白質結構之搜尋功能。因此SARST可以當作一個優良的快速粗略搜尋過濾器，並串聯其他的優質蛋白質結構比對工具當作後處理，最後可以得到快速又正確的搜尋比對結果。

Abstract
The physiological functions of proteins are decided by the molecule structures. Therefore, analysis of protein structures plays an important role in modern biology research. The structure alignment is a powerful tool to compare and find similar proteins. Based on different criteria of different approaches, some protein structure alignment algorithms have been developed, and widely applied to protein structure analysis. The structure alignment method, SARST, which performs sequence alignment on the converted information of Ramachandran plots of proteins, has been proposed to provide fast alignment and searching abilities within a large protein structure database.
In this thesis, we implement SARST and add some enhancements to improve it to be a more applicable software tool and available on Internet. SARST is tested with some real protein structure data from PDB, and analysis of parameters of SARST is included. Although SARST may not offer superior pairwise alignment qualities, it provides a much faster one-against-all searching for similar protein structures. Therefore, SARST can be a good filter to get fast rough searching, combined with other well-defined structure alignment tools as post-processing to get accurate final alignments.

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