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博碩士論文 etd-0820108-215243 詳細資訊
Title page for etd-0820108-215243
論文名稱
Title
蛋白質全原子骨幹結構之預測方法
Refinement of All-atom Backbone Prediction of Proteins
系所名稱
Department
畢業學年期
Year, semester
語文別
Language
學位類別
Degree
頁數
Number of pages
70
研究生
Author
指導教授
Advisor
召集委員
Convenor
口試委員
Advisory Committee
口試日期
Date of Exam
2008-07-14
繳交日期
Date of Submission
2008-08-20
關鍵字
Keywords
預測、骨架、蛋白質
backbone, prediction, protein
統計
Statistics
本論文已被瀏覽 5687 次,被下載 935
The thesis/dissertation has been browsed 5687 times, has been downloaded 935 times.
中文摘要
蛋白質骨幹結構重建問題(PBRP),即是重建出完整包含所有原子(氮、碳及氧原子)的蛋白質骨架。在前人的研究中,我們發現其氧原子的座標預測與其他氮原子和碳原子比較起來,預測準確度明顯地不佳。因此,我們的目標是依據前人的方法給定蛋白質骨幹的氮、碳及氧原子,針對其氧原子的座標加以微調。基於 AMBER 能量立場,我們依據21種胺基酸(包括nonstandard residues)分別去統計原子間的鍵長及鍵角,進而簡化能量公式。再來,我們提出了二階段預測方法(TPRM),依據我們所修改的能量式子,求得最小的能量,進而獨立地找出每一個氧原子的座標。在這裡我們使用兩個測試集來驗證此方法的效能,在實驗結果上顯示,我們方法的重建正確性較前人方法精確;我們的答案亦較為穩定。此外,我們方法的執行時間也快過於著名的預測工具,SABBAC。
Abstract
The all-atom protein backbone reconstruction problem (PBRP) is to rebuild the 3D coordinates of all atoms on the backbone which includes N, C, and O atoms. In the previous work, we find that the prediction accuracy of the 3D positions of the O atoms is not so good, compared with the other two atoms N and C. Thus, our goal is to refine the positions of the O atoms after the initial prediction of N, C, and O atoms on the backbone has been done by the previous work. Based on the AMBER force field, we modify the energy function to a simplified one with the statistical data on the bond lengths and bond angles of the 21 distinct amino acids (including the nonstandard one). Then, we propose a two-phase refinement method (TPRM) to find the position of each O atom independently that optimizes the modified energy function. We perform our method on two test sets of proteins. The experimental results show that the reconstruction accuracy of our method is better than the previous ones. The solution of our method is also more stable than most of the previous work. Besides, our method runs much faster than the famous prediction tool, SABBAC.
目次 Table of Contents
ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0
Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . 1
Chapter 2. reliminaries . . . . . . . . . . . . . . . . . . . . . . . 5
2.1 Properties of roteins . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.1 Amino Acids and Peptides . . . . . . . . . . . . . . . . 5
2.1.2 Levels of Protein Structures . . . . . . . . . . . . . . . 7
2.2 Molecular Mechanics . . . . . . . . . . . . . . . . . . . . . . 10
2.2.1 The AMBER Force Field . . . . . . . . . . . . . . . . . . . 13
2.2.2 The CHARMM Force Field . . . . . . . . . . . .. . . . . 14
2.3 Root Mean Square Deviation . . . . . . . . . . .. . . . . . 16
2.4 Previous Work . . . . . . . . . .. . . . . . . .. . . . . . . .. . . . . 18
2.4.1 MaxSprout . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . 18
2.4.2 Adcock's Method . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.4.3 SABBAC . . . . . . . . . . . . . . .. . . . . . . . . .. . . . . . . . . 20
2.4.4 Wang's Method . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 3. Our Method . . . . . . . . . . . . . . . . . . . . .. . . . . 22
3.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.2 An Overview of Our Method . . . . . . . . . . . . . . . .. . 24
3.3 Refinement of the O Atom Positions on the Backbone . . . . . . . . . . . 24
3.4 The Fitness Function . . . . . . . . . . . . . . . . . . . . . . .. 26
Chapter 4. Experimental Results . . . . . . . . . . . . . . . . 32
Chapter 5. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . 49
BIBLIOGRAPHY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
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