結構生物學分析系統：以BCL串接執行藥物對接（嵌合）與分子動態模擬

Structural Biology Analysis System：Use BCL (Biosym Command Language) to Connect with the Command and to Execute Drug Docking and Molecule Dynamic Simulation

王孝群(Shiao-Chun Wang)

指導教授 ： 龐金宗

共同指導教授 ： 樓 國 隆

元智大學/資訊學院/資訊管理學系/碩士(2006年)

摘要

電腦分子模擬可以用來幫助建立分子模型，並預測或解釋此某一分子的物理性質或化學性質，其中藥物嵌合模擬 (Docking simulation) 可促使或協助藥物能夠快速發展，而且可以觀察到小分子與大分子相互作用模式。在本論文會說明現今分子對接的方法，而依其複雜的程度，可以把分子對接方法分為三大類: Rig-id body docking、Flex-rigid docking、Full-flexible docking。
在本論文中將利用InsightII為平台，並利用Scripting Language BCL (Bios-ym Command Language) 去建立出一連串的自動化嵌合模擬，並且利用ZDOCK的FFT(Fast Fourier Transform)來進行廣度的搜尋比對，找出藥物的可能對接位置，接著再對這一群可能的位置進行MolD (Molecule Dynamics)的運算，接著在利用MolD (Molecule Dynamics)所運算出的數據和原有的蛋白質(當初所找到可能的位置)及藥物做RMSD的計算，並與各種能量和時間做相關的分析。

關鍵字

藥物嵌合模擬，自動化嵌合模擬，分子對接，ZDOCK，分子動態模擬

並列摘要

The molecule simulation can be used to help to build the molecule mode, predict, and explain physical character or chemical character. Docking simulation, moreover, can be used to move or help medicine to develop fast, and to observe the interaction between the ligand and the biomacromolecuar. In this thesis, the molecule docking method will be stated, including Rigid-body docking、Flex-rigid docking and Full-flexible docking. We will also use Scripting Language BCL (Biosym Command Language) to create automatic processes
and to predict the interaction of ligand with biomacromolecular targets on an
infrastructure of Insight II. There will be two approaches mentioned in this
thesis – ZDOCK and MolD (Molecule Dynamics). We will use ZDOCK first to search and to compare conformational space, and to find a probable position. Then, we will use MolD (Molecule Dynamics) to calculate the part energy and RMSD of this probable position.

並列關鍵字

Docking simulation,molecule simulation,molecule docking,Molecule

參考文獻

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