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研究生： 游景仁
Jing-Ren Yu
論文名稱： 蛋白質註解的三維視覺化工具
PAI3D:3D Visualization Tool for Protein Annotations
指導教授： 何錦文
Chin-Wen Ho
口試委員:
學位類別： 碩士
Master
系所名稱： 資訊電機學院 - 資訊工程學系
Department of Computer Science & Information Engineering
畢業學年度： 92
語文別： 英文
論文頁數： 64
中文關鍵詞： 三維視覺化工具 、蛋白質註解
外文關鍵詞： visualization, PAI3D, Chime, protein annotation
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    • 蛋白質註解是幫助生物資訊科學家和生物學家了解蛋白質功能的重要資訊. 我們發展了一個使用Chime外掛程式, 名叫PAI3D 的蛋白質註視覺化網頁伺服系統. 此系統用來整合蛋白質註解並將蛋白質註解視覺化在3D 分子結構上觀察.
    在此系統中, 首先透過一個中介的網路資料擷取代理程式, 從蛋白質註解相關網站的網站中, 將蛋白質註解擷取出來. 每個資料擷取代理程式對應一個網站. 目前我們系統中有9個資料擷取代理程式. 系統有提供機制允許使用者新增資料擷取代理程式到系統內. 當資料從代理程式擷取後,我們將含有結構化資訊的蛋白質註解轉換成一連串的Chime控制命令碼以用來控制蛋白質3D呈現樣式. Chime控制命令碼指示了明確的蛋白質3D結構上,蛋白質註解所表現形式, 包括所表現的區域, 表現色彩, 表現形狀, 以及呈現的標籤文字.
    雖然Chime 本身有內建基本的蛋白質樣式操縱功能, 我們仍可用Chime提供的控制命令碼(scripts)來設計出一些獨特網頁上蛋白質的互動應用工具. 這些工具目標是提供更佳的操作介面以及一個用來更進一步觀察蛋白質的輔助工具.

    Protein annotations are crucial for bioinformatics scientists and biologists to understand protein functions. We develop a Chime plug-in based web server which is a 3D visualization system called PAI3D for protein annotations integration and visualizing protein annotations through the 3D visualization tool.
    In this system, protein annotations are initially extracted from related protein annotation websites through Web wrappers. Each wrapper corresponds to one website. For this moment, there are nine wrappers in the PAI3D system. However, the system allows users to add their own wrappers. After data extraction from wrappers, the system transforms protein annotations data into a series of Chime script commands for controlling the display style of protein 3D structure in the viewer. Chime script commands indicate precise annotation display styles on protein 3D structure, including display region, display colors, display shapes, and display text labels.
    Although Chime itself provides basic built-in protein display manipulation functions, we also use Chime scripts to design several unique web-based protein interactive applications. These applications aim to provide a better interface and a helper tool for protein advanced observation.

    Chapter 1 Introduction...........................................1 1.1 Background...................................................2 1.1.1 Protein molecular structure................................2 1.1.2 Protein 3D visualization tools.............................4 1.2 Motivation...................................................7 1.3 Research goals...............................................9 Chapter 2 Materials & Related Works.............................10 2.1 Database lists..............................................10 2.2 Web Wrapper Tool............................................11 2.3 Chime Plug-in...............................................14 2.3.1 Features, function, manipulation of Chime.................15 2.3.2 Chime and RasMol Scripts..................................15 2.3.3 MDL Chime embed tags......................................16 2.3.4 Mechanism of Chime interaction............................16 Chapter 3 Methods...............................................17 3.1 System overview.............................................17 3.2 Protein annotations extraction by wrappers..................19 3.3 Converter...................................................25 3.3.1 Extended Swiss-Prot format................................26 3.3.2 Conversion from the 3D visualizable annotations file to the extended Swiss-Prot file...........................29 3.4 Parser......................................................32 3.5 Visualization tool generator................................33 Chapter 4 Results...............................................35 4.1 Automatic visualizing protein annotations system............35 4.1.1 Display of 3D visualizable protein annotations............39 4.1.2 Display of 3D unvisualizable protein annotations..........43 4.1.3 Adding a new protein annotation database source...........44 4.2 Protein 3D visualization toolkit............................45 Chapter 5 Conclusion............................................52 5.1 Discussion..................................................53 5.2 Future works................................................54 References......................................................55 Web Site References.............................................56

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