臺灣博碩士論文加值系統

蛋白質結構在我們了解此蛋白質的功能上扮演著非常重要的角色。而從蛋白質的一級序列預測其三級結構在生物資訊領域中也有著重要的幫助。蛋白質的真實結構可經由一些極耗費時間及成本的技術取得，但蛋白質結構預測可幫助我們預先判斷此蛋白質的功能。在這裡我們發展出三項數值可以運用在蛋白質骨幹結構預測上的效益評估函數。從結果中可以顯示，我們經由GP(Genetic Programming)產生出來的效益評估函數於CASP8競賽中的蛋白質預測序列中有80%高於平均值。

For understanding the function of a protein, the protein structure plays an important role. The prediction of protein structure from its primary sequence has significant assistance in bioinformatics. Generally, the real protein structures can be reconstructed by some costly techniques, but predicting the protein structures helps us guess the functional expression of a protein in advance. In this thesis, we develop three terms as the materials of the fitness function that can be successfully used in protein backbone structure prediction. In the result of this thesis, it shows that over 80% of good values calculated from our fitness function, which are generated by the genetic programming, are better than the average in the CASP8.

ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0
Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Chapter 2. Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1 Amino Acids in Proteins . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2 Levels of Protein Structures . . . . . . . . . . . . . . . . . . . . . . . 4
2.3 Conformational Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.4 Protein Structure Prediction Methods . . . . . . . . . . . . . . . 10
2.5 Sequence Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.6 Genetic Programming . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.7 Root Mean Square Deviation . . . . . . . . . . . . . . . . . . . . . . 17
2.8 Critical Assessment of Protein Structure Prediction . . . . . . . . . . 20
Chapter 3. Our Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Chapter 4. Experimental Results . . . . . . . . . . . . . . . . . . . . . .31
Chapter 5. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
BIBLIOGRAPHY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

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