- 學位論文
利用動態時間扭曲及最小二乘平差分析殘基接觸以比對蛋白質結構
Rsidue Contact with Dynamic Time Warping and Least Squares Adjustment for Protein Structure Alignment
摘要
在蛋白質研究中，蛋白質結構比對(protein structure alignment)是一個非常重要的議題。一般來說，這個工作可以分為兩個方向，局部結構和整體結構的比對。在本研究中提出由原始蛋白質結構中所得到的殘基接觸(residue contact)，將蛋白質的三維座標轉換為一維的特徵值，接著使用一種迭代的方法,把三維空間中的蛋白質，做整體結構的比對。此一混合方法，結合了動態時間扭曲(dynamic time warping)和最小二乘平差(least squares adjustment)。首先使用動態時間扭曲將兩條蛋白質做粗略的比對，找出對應的關係，再找出其中一對一的組合，以最小二乘平差解出旋轉平移參數，使得兩條在不同空間維度的蛋白質，轉換座標至同一維度空間並修正座標。計算轉換後的誤差量為權重，加速粗略到精細比對的速度，並計算其均方根偏差值(RMSD)，經過迭代至收斂後，輸出轉換後之座標，即為最終最佳胺基酸配對之對應。
並列摘要
Protein structure alignment is one of important issues in protein study. In general, such task can be divided into two categories, i.e. global and local structure alignment. In this paper, the proposed residue contact is extracted from original protein structure. A hybrid approach combining dynamic time warping and least squares adjustment is proposed for global alignment of protein 3D structures in an iterative fashion, where dynamic time warping is responsible for coarse alignment of two structures and least squares adjustment handles the fine matching of amino acid residues. The residuals of matched pairs are utilized to calculate the weights to accelerate the convergence of coarse-to-fine matching. The matched amino acid residues are transformed to the same coordinate system for calculating RMSD value. The preliminary results have demonstrated the effectiveness and efficiency of the proposed approach.