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研究生:賴文忠
研究生(外文):Wen-Chung Lai
論文名稱:利用核磁共振化學位移之二維分析預測蛋白質二級結構與胱胺酸氧化還原狀態之網路伺服器
論文名稱(外文):A Web-based Server for Predicting the Secondary Structures of Proteins and Redox States of Cysteine by Using 2D NMR Chemical Shifts
指導教授:王清正
指導教授(外文):Ching-Cheng Wang
學位類別:碩士
校院名稱:國立成功大學
系所名稱:製造工程研究所碩博士班
學門:工程學門
學類:機械工程學類
論文種類:學術論文
論文出版年:2006
畢業學年度:94
語文別:中文
論文頁數:59
中文關鍵詞:NMR二級結構預測化學位移氧化還原狀態
外文關鍵詞:chemical shiftsNMRpredictionredox statessecondary structure
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  • 被引用被引用:0
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  • 下載下載:39
  • 收藏至我的研究室書目清單書目收藏:0
2DCSi利用核磁共振化學位移(NMR chemical shifts),包含1Hα、1HN、13Cα、13C’、15NH等原子相對於13Cβ原子的二維叢集分析(2D cluster analyses),來預測20種胺基酸的二級結構,與胱胺酸(Cysteine,Cys)的氧化還原態(redox states)。
我們從BioMagResBank (BMRB)資料庫提供的檔案中擷取每一個胺基酸的1Hα、1HN、13Cα、13C’、15NH、13Cβ原子的化學位移,建立計分矩陣(scoring matrix),以此計分矩陣為基礎,使用者可利用我們架設之2DCSi伺服器,輸入胺基酸化學位移資料、或上傳BMRB檔案,來預測其二級結構與胱胺酸之氧化還原狀態。
2DCSi server網址:http://ncku.2dsci.idv.tw。
2DCSi predicts the secondary structures of 20 amino acids and the redox states of cysteine residues in proteins by using their NMR chemical shifts.
We use 2D cluster analyses of 1Hα, 1HN, 13Cα, 13C’, and 15NH versus 13Cβ NMR chemical shifts which were constructed from BioMagResBank (BMRB) entries. A database of 20 amino acids’ 1Hα, 1HN, 13Cα, 13C’, 15NH, and 13Cβ NMR chemical shifts were obtained and then used to produce the scoring matrices. Applying the prediction rules, the 2DCSi server enables users to submit NMR chemical shifts data and to request protein secondary structure assignments and the redox states of cysteine residues.
2DCSi server is available at http://ncku.2dsci.idv.tw.
摘 要.................................................................I
Abstract..............................................................II
誌 謝................................................................III
圖目錄.................................................................V
表目錄................................................................VI
第一章 緒論............................................................1
1.1 研究動機與重要性...................................................1
1.2 研究背景...........................................................2
1.3 研究目的...........................................................3
第二章 文獻探討........................................................4
2.1 化學位移(Chemical Shifts)..........................................4
2.2 二級結構指派(Secondary Structure Assignment).......................5
2.3 胱胺酸之氧化還原狀態(Redox State of Cysteine)......................6
第三章 研究方法及步驟..................................................8
3.1 化學位移資料收集(Data Collection)..................................8
3.2化學位移之叢集分析(Cluster Analyses)................................9
3.3計分矩陣( Scoring Matrices ).......................................11
3.3.1胱胺酸之計分矩陣(Scoring Matrices of CYS)........................11
3.3.2 其他胺基酸之計分矩陣(Scoring Matrices of Other Amino Acids).....12
3.4 2DCSi方法與程式邏輯(2DCSi Method and Program).....................13
3.4.1 單殘基預測......................................................13
3.4.2 上傳BMRB檔案預測................................................15
3.4.3 預測結果之顯示..................................................19
第四章 2DCSi預測結果..................................................20
第五章 結論與未來展望.................................................22
參考文獻..............................................................23
附錄一 2DCSi網站使用說明文件..........................................25
附錄二 25 測試檔案....................................................32
自 述.................................................................59
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