测定蛋白质模板中不连续片段之结构相似度Determiningthesimilarity.PDF

Journal of Information Technology and Applications Vol. 8, No. 3, pp. 56-62 2014 測定蛋白質模板中不連續片段之結構相似度 Determining the similarity of discrete fragments in protein structural motif 楊凱傑、董其樺* 中華大學生物資訊學系 新竹市香山區東香里五福路二段 707號 電話： 03-5186782 傳真：03-5186416 Email ：chihua.tung@chu.edu.tw Kai-Chieh Yang, Chi-Hua Tung* Department of Bioinformatics, Chung Hua University, Hsinchu, Taiwan, R.O.C. 摘要 在目前結構比對領域中，有許多研究者致力於開發高效率、高準確性比對蛋白質的結構演算法，但較少 演算法可提供在空間中多個不連續片段的結構比對。本論文針對此議題提出一個利用距離幾何演算法應用於 比對多片段在空間的所形成的幾何構形，進而探究蛋白質模板結構相似度計算與評估。本論文之方法主要為 研究點座標在三維空間中構形的相似程度，演算過程中考慮所有可能出現的子幾何形狀組合，利用旋轉矩陣 進行平移疊合，再透過比對相似度判斷應剔除的點座標，進而輸出在空間中正確對應的蛋白質模版結構，確 認其結構相似度。 關鍵字 :局部結構比對、分子距離幾何、蛋白質模板搜尋 ABSTRACT In the area of structural bioinformatics, many researchers dedicated to develop protein structure alignment algorithms which are highly efficient and accurate, but fewer algorithms may provide capability to align discrete segments in the space. This researd proposed a methodology of distance geometry that is applied to superimpose discriminative fragments by exploring and calculating protein structure motifs similarity. In this study, the conformation similarity of the coordinates in Euclidean space is identified. We considered all combinations of sub-graph geometry, and applied rotation matrix to superpose sub-graphs. Then, we distinguished the selectivity of coordinates in multiple fragments by the similarity, and obtain the set of correct motifs. Keywords