蛋白質支鏈結構預測是蛋白質三級結構預測中重要的一環，蛋白質支鏈結構預測問題已被證明是NP-hard，此一複雜問題可以轉化為尋找完全子圖的問題，並使用螞蟻演算法求得近似最佳解。我們先建立一個rotamer library作為模板，再根據主鏈上的兩個雙面角ψ和φ，為每個胺基酸位置找到一個適當的rotamer，接著用計分函式判斷螞蟻演算法所得解的好壞。我們的計分函式考慮了雙硫鍵、分子間氫鍵、電荷間作用力及凡得瓦力等因素對蛋白質支鏈結構的影響，實驗結果顯示，我們的計分函式可分辨預測結果是否為穩定的三級結構，具有生物上的意義。
將我們的預測方法與SCWRL 3.0及R3兩種方法比較，雖然在執行速度上不及兩者，但是有較高的準確率。

The protein side chain prediction is an essential issue, in protein structure prediction, protein design, and protein docking problems. The protein side chain packing problem has been proved to be NP-hard. Our method for solving this problem is first to reduce it to the clique finding problem, and then we can apply the Ant Colony Optimization (ACO) algorithm to solve it. In knowledge-based methods, the rotamers are chosen from the rotamer library, which are
based on the pair of dihedral angles, ψ and φ, of backbones. We take the coordinate rotamer library as the template, so we do not need the complicated energy function to calculate the bond length and bond angle. We use a simple score function to evaluate the goodness of a solution of the ACO algorithm. The score function combines some factors, such as charge-charge interaction, intermolecular hydrogen bonds, disulfide bonds and van der Waals interactions. The experimental results show that our score function is biologically sensible. We compare our computational results with the results of SCWRL 3.0 and the
residue-rotamer-reduction (R3) algorithm. The accuracy
of our method outperforms both SCWRL 3.0 and R3 methods.

LIST OF FIGURES . . . . . . . . . . . . . . . . . . . . . 3
LIST OF TABLES . . . . . . . . . . . . . . . . . . . . . 4
ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . 0
Chapter 1. Introduction . . . . . . . . . . . . . . . . . 1
Chapter 2. Preliminaries . . . . . . . . . . . . . . . . 4
2.1 Properties of Proteins . . . . . . . . . . . . . . . 4
2.2 PreviousWorks . . . . . . . . . . . . . . . . . . . 13
2.3 Ant Colony Optimization Algorithm(ACO) . . . . . . . 14
Chapter 3. The Method for Side Chain Determination . . . 18
3.1 The Definition of the Protein Side Chain Packing Problem . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.2 The Overview of Our Algorithm . . . . . . . . . . . . 20
3.3 The Rotamer Library . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.4 The Score Function . . . . . . . . . . . . . . . . . . . . . . . . 25
Chapter 4. Experimental Results . . . . . . . . . . . . . 30
Chapter 5. Conclusion . . . . . . . . . . . . . . . . . . . . . . . 34
BIBLIOGRAPHY . . . . . .. . . . . . . . . . . . . . . . . 35

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