分子模擬與藥物設計的概論與應用
Molecular modeling and computer-aided drug design: Principles and Applications
| 節 | 週四 |
|---|---|
5 13:20–14:10 | 分子模擬與藥物設計的概論與應用 YK104 2 節連堂 |
6 14:20–15:10 |
* 根據陽明交大上課時間表所列
本課程主題包括: 生物分子結構與功能關係，結構生物學資料庫，量子力學，分子力學，力場原理，位能面，能量最佳化演算法，統計力學，分子動力學模擬和蒙地卡羅原理，藥物設計，生物奈米材料電子元件設計及藥物設計實作。分子動力學模擬方法已經是生物分子理論研究的主要工具之一。分子動力學模擬計算方法可用於研究分子系統與時間相關的物理性質，提供有關蛋白質和核酸的結構變化的詳細資訊。這些方法用於研究生物分子及其複合物的結構、動力學和熱力學等性質，及輔助X射線晶體和NMR實驗分子結構建立。學習者將獲得原理與應用和實作訓練，包括：搜索蛋白質數據庫，建立分子結構，能量最佳化，執行分子動力學以及結構與能量分析。The course covers the concepts of molecular modeling and simulation. The topics include an overview of structure database, statistical mechanics, quantum mechanism, molecular mechanism, force field, potential energy surface, energy minimization, classical molecular dynamics simulations, and Monte Carlo methods to discuss some practical aspects of the method and to provide several specific applications. The method of molecular dynamics simulations is one of the principal tools in the theoretical study of biological molecules. This computational method is used to study the time dependent behavior of a molecular system. Molecular dynamics simulations can provide detailed information on the fluctuations and conformational changes of proteins and nucleic acids. These methods are used to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes, and also used in the determination of structures from x-ray crystallography and from NMR experiments. The students will obtain practical knowledge and operation including: to search protein data bank, generate 3D structures, perform energy minimization, and perform molecular dynamics, and conformation/energy analysis.
本課程規畫給生命科學、生物化學、藥學和生醫材料相關的學生及對分子動力學模擬計算有興趣的研究學者。教學目標為學習如何檢索相關結構生物學資料庫及生物分子系統模擬基本原理與應用、生物分子結構建立、藥物設計、分子辨識及生物奈米材料電子元件設計與應用。利用電腦模擬技術方法與工具，來探討生物巨分子之結構及其結構與功能之間的關係。This course is designed for life science, biochemistry, pharmacy, and biomedical material students and research scientists, who are interested in molecular dynamics simulations. The course topics include basic principles and applications of molecular simulation, molecular modeling, drug design, molecular docking, and bio-nanomaterial, electronic devices design, and application. We can use computer simulation techniques and tools to explore the structure of biological macromolecules and the relationship between structure and function.
期末口頭報告 100 分oral presentation 100 points
| 週次 | 主題 |
|---|---|
| 第 1 週 | Introduction (分子模擬介紹) |
| 第 2 週 | Quantum Mechanics (量子力學原理) |
| 第 3 週 | Quantum Mechanics and drug design (量子力學原理和藥物設計) |
| 第 4 週 | Molecular Mechanics (分子力學) |
| 第 5 週 | Empirical Force Field Models (分子力場與位能面) |
| 第 6 週 | 校際活動 |
| 第 7 週 | Methods of Energy Minimization (能量最佳化的演算法) |
| 第 8 週 | Statistical Mechanics (統計力學概論) |
| 第 9 週 | Algorithms of Molecular Dynamics Simulation (演算法) |
| 第 10 週 | Methods of Molecular Dynamics Simulation (分子模擬方法) |
| 第 11 週 | Computer-aided drug design (藥物設計原理) |
| 第 12 週 | Computer-aided drug design (藥物設計原理) |
| 第 13 週 | AI application in drug design (人工智能平台藥物設計) |
| 第 14 週 | Demonstrations (分子模擬模組操作) |
| 第 15 週 | Demonstrations (分子模擬模組操作) |
| 第 16 週 | Final Exam (期末考) |
教科書名：1. Molecular modeling: Principles and Applications (Andrew R. Leach). 作 者：1. Andrew R. Leach