目前以分子動力學模擬軟體之參數，多是取自於實驗量測之結構加以統計分析，或是用軟體模擬小型結構進而套用，而這些參數也常被應用於同源模擬法之初始結構排列。從統計結果我們可以知道，蛋白質之中的各種鍵長與角度可能會因為各種環境因素之影響而呈現不同分布，而分類若能越詳細，則越能探究這些環境因素與蛋白質結構的關係，在應用這些參數時則可以依據分子的環境，較精確的挑選參數，以達到較好的預測效果。本研究探討區塊為單純之二級結構環境與胺基酸結構的關係，是以詳細內容的二級結構作為單一胺基酸環境的分類依據，並且用已知的條件將其分類，之後將各個分類群組之中胺基酸的鍵長、鍵角及兩面角計算其平均值，將其拼湊後可得胺基酸的平均結構樣板，即可依照類別挑選套用於初始結構，若要加以統計分析，則僅需挑選出欲分析或比較的群組數值即可進行分析。

Simulations using molecular dynamics (MD) ands homology modeling are applied to predicting protein conformations. Presently, geometric parameters of amino acids needed to initiate MD simulations such as bond-lengths and angles are often obtained from analyzing experimental results or modeling them by calculating small molecular structures. Previous analysis reveals that bond-lengths, bond-angles, and other geometric parameters are affected by the secondary structure of a protein, and other factors as well. Rotational isomer (Rotamer) libraries have attempted to capture the effect of the secondary structure on certain geometric parameters. Unfortunately, rotamer libraries consider only a partial of side chain dihedral angles, and parameters such as bond-lengths and angles are left behind. For the remedy, this research aims at establishing a compete library including every protein geometric parameter that is considered to be affected by the secondary structure. In this effort, we employ DSSP and Stride while conducting assignments. It is well known that not all the assignment results by both methods are consistent. To avoid unnecessary errors caused by assignment inconsistency, inconsistent results are excluded from our investigation. We calculate sample mean and standard deviation of bond-lengths, bond-angles and dihedral angles of each amino acid. Those statistics could be applied while building the nominal conformation of each type of amino acids, and the nominal conformation could then be applied while generating the initial conformation as needed by MD simulations.

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