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研究生:許育堂
研究生(外文):Yu-Tang Syu
論文名稱:以溶劑可接觸面積預測結果為基礎分析蛋白質之間的交互作用
論文名稱(外文):Analyzing Protein-Protein Interactions based on Predicted Accessible Surface Area
指導教授:張天豪
指導教授(外文):Tien-Hao Chang
學位類別:碩士
校院名稱:國立成功大學
系所名稱:電機工程學系碩博士班
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:44
中文關鍵詞:蛋白質之間交互作用溶劑可接觸面積
外文關鍵詞:accessible surface area (ASA)protein-protein interaction (PPI)solvent accessibility
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了解蛋白質之間交互作用的機制可以幫助我們建構蛋白質交互作用網路以及釐清生物系統的運作原理。先前的研究顯示出透過分析蛋白質一級結構-胺基酸序列-可以有效預測蛋白質交互作用,這些以序列為基礎(sequence-based)的方法,相較於其他需要額外資訊(如蛋白質結構、基因表現等)的方法,提供了更廣泛的應用範疇。
本論文提出一個新的以序列為基礎來預測蛋白質交互作用的方法,該方法依據蛋白質之間交互作用與位於表面之氨基酸的相關程度比其它位於核心的胺基酸來的高,因此在預測時考慮了蛋白質的表面資訊。為了延續只使用序列資料的優勢,本研究使用一套以序列為基礎之溶劑可接觸面積(accessible surface area, ASA)預測器來決定蛋白質表面。實驗結果顯示表面資訊確實可以幫助預測蛋白質之間交互作用,本研究亦分析了使用ASA預測器所預測出的蛋白質表面與透過結構所獲得的蛋白質表面之間的差異,實驗結果顯示使用ASA預測器的蛋白質表面,在預測蛋白質交互作用時準確度僅略低於透過結構所獲得的蛋白質表面。
In this study, we demonstrate a mechanism of predicting protein-protein interactions that is essential to construct protein interaction networks and assist researchers to understand the characteristic of the general principles of biological systems. Previous studies have shown that interacting protein pair can be predicted by its primary structure. These sequence-based methods provide broader applications than those require both additional information and protein sequences.
This work presents a novel sequence-based method based on an assumption that the protein-protein interactions are more related to amino acids at the surface than those at the core. This study utilizes the accessible surface area predictor (ASA) predictor to decide protein surface. The predicted surface information can help to predict protein-protein interactions. This study also analyzes the performance of using the predicted surface by the ASA predictor in comparison with that using the surface obtained from structures.
摘 要 I
目 錄 IV
表目錄 VI
圖目錄 VII
CHAPTER 1 緒論 8
CHAPTER 2 相關研究 9
2.1蛋白質 9
2.2 ASA 13
2.3預測蛋白質交互作用方法 14
CHAPTER 3資料集與實驗方法 21
3.1資料集 21
3.2 預測流程 22
3.2.1 ASA預測 23
3.2.2蛋白質表面預測 25
3.2.3特徵編碼 26
3.3分類工具 27
CHAPTER 4 實驗結果與討論分析 29
4.1預測效能評估準則 30
4.2不同的蛋白質表面定義對預測蛋白質交互作用結果之影響 31
4.3 ASA估計值與實際值預測蛋白質之間交互作用結果之影響 33
4.4評估蛋白質表面區塊預測之好壞 34
4.5評估蛋白質之間交互作用的接合面區塊預測之好壞 36
4.6不同資料比例的影響 38
CHAPTER 5結論與未來展望 40
5.1 結論 40
5.2 未來展望 40
參考文獻 41
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