Introduction to structural bioinformatics
Fundamentals of protein structure
The Protein Data Bank
Molecular visualization
Structure-based databases
Protein evolution and the SCOP database
The CATH domain structure database
Structure quality assurance
Midterm (Oral Presentation)
Structure comparison and alignment
Secondary structure assignment
Identifying structural domain and function in proteins
Prediction of protein-protein interaction
Principles and methods of docking and ligand design
Homology modeling
Fold recognition method
Prediction in 1D : secondary structure, membrane helices and accessibility
Final project
教學目標Course Objectives
「結構生物資訊」是以結構的角度對蛋白質進行生物資訊之研究。課程除了介紹數種在網路相關的分析工具以及資料庫,例如: Protein Data Bank (PDB) (存放蛋白質結構的資料庫)、DSSP (介紹蛋白質二級結構的資料庫)、SCOP and CATH (依照蛋白質結構分類的資料庫)、Rasmol和Pymol (顯示蛋白質結構的視覺化軟體) 外;還會介紹結構生物資訊最新、最熱門的研究主題以及目前發展的現況,其中包括structure comparison and alignment (蛋白質結構比對)、homology modeling (利用蛋白質同源模擬結構)、 fold recognition (蛋白質摺疊辨識法) 以及 structural prediction (蛋白質結構預測)。本課程的目標在於讓學生認識各種蛋白質結構在生物資訊上的議題,且能利用所教授的軟體與資料庫來進行專題研究。
The purpose of this course will focus on the issues of the Structural bioinformatics. Various tools and databases that are well developed and published on the websites will be introduced. These databases or tools include Protein Data Bank (PDB), Protein structure (DSSP), Structural Classification of Protein (SCOP and CATH), Rasmol and Pymol. The students are required using the public software or databases to answer the questions that the lecturer assigns, including finding structure, structure comparison and alignment, homology modeling, fold recognition and structural prediction.
先修科目Prerequisites
無
none
教學方式Teaching Methods
評量方式Assessment
Midterm (40%) and Final project(60%)
參考書目Reference
Structural Bioinformatics: 2003, edited by Philip E. Bourne, Helge Weissig
教學進度Course Schedule
2014/02/18 結構生物資訊學入門
Introduction to structural bioinformatics
陸志豪(Chih-Hao Lu) 2014/02/25 PDB (蛋白質資料銀行)
Protein Data Bank
陸志豪(Chih-Hao Lu) 2014/03/04 分子結構視覺化
Molecular visualization
陸志豪(Chih-Hao Lu) 2014/03/11 分子結構視覺化
Molecular visualization
陸志豪(Chih-Hao Lu) 2014/03/18 蛋白質結構之相關資料庫
Structure-based databases
陸志豪(Chih-Hao Lu) 2014/03/25 蛋白質演化與蛋白質結構分類SCOP資料庫
Protein evolution and the SCOP database
陸志豪(Chih-Hao Lu) 2014/04/01 辨識蛋白質結構的品質與動態特性
Structure quality assurance
陸志豪(Chih-Hao Lu) 2014/04/08 蛋白質結構比對
Structure comparison and alignment
陸志豪(Chih-Hao Lu) 2014/04/15 期中考
Midterm
陸志豪(Chih-Hao Lu) 2014/04/22 蛋白質二級結構分類
Secondary structure assignment
陸志豪(Chih-Hao Lu) 2014/04/29 辨認蛋白質功能區域
Identifying structural domain and function in proteins
陸志豪(Chih-Hao Lu) 2014/05/06 預測蛋白質交互作用
Prediction of protein-protein interaction
陸志豪(Chih-Hao Lu) 2014/05/13 藥物及接合子對接之準則及方法
Principles and methods of docking and ligand design
陸志豪(Chih-Hao Lu) 2014/05/20 三級結構預測之同源模擬
Homology modeling
陸志豪(Chih-Hao Lu) 2014/05/27 蛋白質摺疊辨識法
Fold recognition method
陸志豪(Chih-Hao Lu) 2014/06/03 從蛋白質序列中預測二級結構,膜蛋白螺旋及親水性
Prediction in 1D : secondary structure, membrane helices and accessibility
陸志豪(Chih-Hao Lu) 2014/06/10 分子模擬
Molecular simulation
陸志豪(Chih-Hao Lu) 2014/06/17 期末專題
Final project
陸志豪(Chih-Hao Lu)