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研究生:黃加穎
研究生(外文):Huang Chia-Yin
論文名稱:應用基因演算法於胺基酸序列最適能量之計算
論文名稱(外文):Computing the optimal energy of a polypeptide using a genetic algorithm
指導教授:林志侯
指導教授(外文):Lin Thy-Hou
學位類別:碩士
校院名稱:國立清華大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:中文
論文頁數:52
中文關鍵詞:基因演算法胺基酸序列交配突變選擇
外文關鍵詞:genetic algorithmcrossovermutationselectionECEPPMet-enkephalinPolyalaninesPolyglycines
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欲瞭解蛋白質的三級結構( conformation )必須利用 X-ray 或 NMR 的方法,這兩種方法都相當費時又需要耗費大量的資源,因此研究人員希望利用電腦快速地預測出其構形,以瞭解此蛋白質在生物體內所產生的功能( function )。目前此領域遭遇到最大的困難在於其可能形成的結構數目太過龐大,複雜的程度遠非電腦所及,同時容易陷入”局部極小”( local minimum )而非”全域極小”( global minimum )
的能量值,導致無法求出正確的結構解。
基因演算法則( Genetic Algorithm )以模擬大自然的演化原理,交配( crossover )、突變( mutation )、選擇( selection )之物競天擇、適者生存方式來進行資料最佳化的搜尋,它能夠選擇物種中具有較好特性的上一代母代,並且隨機性的相互交換彼此的位元資料,以期能產生比上一母代更優秀的子代,如此重複下去以產生適應性最強的最佳物種。本研究先嘗試以胺基酸序列( peptide )為主題,結合ECEPP ( Empirical Confirmation Energy Program for Peptides )此軟體所計算的能量值,發展出一套基因演算法的電腦程式來篩選出最合適的能量解,同時預測其可能的構形,並且很成功地計算出五個胺基酸序列 Met-enkephalin ( Tyr-Gly-Gly-Phe-Met )以及多結構的polyalanines、polyglycines所公認的能量值,未來可更進一步計算較大蛋白質之能量與其可能之形狀。

The X-ray or NMR methods are usually used to get the tertiary structure of protein . Both of them are time-consuming and needed a lot of resource . Therefore , the researchers wish to utilize computers to predict the conformation structure more quickly , and then to study the function of protein produced in biological organism . At present , the difficulty of this field is the total conformations are too numerous , and it is so complicated that would be out of current computation power . Meanwhile , the convergent energy is another problem .It often converges to a so- called " local minimun " , not the " global minimun " energy , and could not get the exact solution of that structure .
Genetic algorithm uses the evolutionary principle to simulate our natural environment . Like species they struggle for survival among things by the law of natural selection , only the survival of the fittest can live. So does this algorithm . It is composed of three major subroutines , CROSSOVER、MUTATION、SELECTION to search for the optimal elite . The method is to select a good character from mother generation and change their bits at random to each other for new one . Sometimes the new generations may have more chances to survive . Generations after generations , we must get the best individual finally . Our research goal is try to make a topic of amino acid sequence and develop a computer program by using this algorithm . We also combine this with one software named ECEPP ( Empirical Confirmation Energy Program for Peptides ) to calculate the energy and produce the conformation . The well-known structure of Met-enkephalin which is made of five amino acid residues( Tyr-Gly-Gly-Phe-Met ) and is computed .We have obtained the exact solution successfully . In future , we may apply it to more complicated polypeptides .

中文摘要….……...……………………..……………………………..Ⅰ
英文摘要………....…………………………..………………………..Ⅱ
目錄………....…………………………..……………………………...Ⅲ
圖目錄………....…………………………..…………………………..Ⅳ
表目錄………....…………………………..…………………………..Ⅴ
第一章 緒論………….…………………………..…………………..1
1.1 蛋白質簡介……………….….……………..…………………...1
1.2 ECEPP簡介……………….……………………………………..3
1.3 程式簡介………..……….………………….…………………...6
第二章 實驗原理和方法…..……..………………………………..7
2.1 基因演算法……………....…….………………………..…….….7
2.2 程式的架構解析和電腦配備……..……….…………...…..….15
第三章 結果……..…….………..…….………………………….…18
第四章 討論……..….………………………………………………29
第五章 參考資料…………..…....…………….…………………...32
附錄一 ECEPP輸出入檔格式…….……………………………40
附錄二 程式原始碼………..…...…………………………………44
附錄三 Met-enkephalin 之PDB檔……….……………….…50

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