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課程名稱 |
結構生物資訊學
Structural Bioinformatics |
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開課學期 |
100-1 |
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授課對象 |
生物資源暨農學院 生物產業機電工程學研究所 |
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授課教師 |
陳倩瑜 |
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課號 |
BME5412 |
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課程識別碼 |
631 U3140 |
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班次 |
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學分 |
3 |
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全/半年 |
半年 |
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必/選修 |
選修 |
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上課時間 |
星期二6,7,8(13:20~16:20) |
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上課地點 |
知203 |
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備註 |
總人數上限：50人 |
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Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1001StruBioinfo |
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課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
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課程大綱
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課程概述 |
此一課程在於介紹計算結構生物學之演算法與生物研究相關之計算工具與資料庫。序列比對演算法如BLAST, 序列資料庫如Swiss-Prot, 結構資料庫如PDB, 結構預測軟體如Rosetta等, 都會在課堂上有詳細的解說, 並搭配作業讓同學更加熟悉生物資訊與相關演算法的使用。 |
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課程目標 |
認識結構生物資訊學，使學生獲得從事生物資訊研究必須之基礎能力。 |
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課程要求 |
作業(包括熟悉並使用linux指令/撰寫簡單scripts/perl程式撰寫)，考試，專題 |
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預期每週課後學習時數 |
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Office Hours |
每週五 13:00~14:00
每週二 13:00~14:00 備註： (建議先使用email約時間) |
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指定閱讀 |
上課講義 |
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參考書目 |
Exploring Bioinformatics: A Project-Based Approach
by Caroline St. Clair
Publisher: Jones & Bartlett Publishers; 1 edition (February 16, 2009)
ISBN: 0763758299
Structural Bioinformatics: An Algorithmic Approach (Chapman & Hall/Crc
Mathematical and Computational Biology Series)
by Forbes J. Burkowski
Publisher: Chapman & Hall/CRC; 1 edition (October 30, 2008)
ISBN: 1584886838
Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure
Analysis
by Ingvar Eidhammer, Inge Jonassen, William R. Taylor
Wiley; 1 edition (March 1, 2004)
ISBN-10: 0470848391
ISBN-13: 978-0470848395 |
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評量方式
(僅供參考) |
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No. |
項目 |
百分比 |
說明 |
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1. |
作業 |
40% |
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2. |
期末專題 |
30% |
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3. |
期中考 |
30% |
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週次 |
日期 |
單元主題 |
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第1週 |
09/13 |
Introduction to Structural Bioinformatics (HW0: learning Perl) |
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第2週 |
09/20 |
Genomics Basics (HW1: transcription and translation) |
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第3週 |
09/27 |
Biological databases and sequence alignment (HW2 database parsing: Uni-Prot) |
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第4週 |
10/04 |
Sequence alignment and clustering (HW3: collecting protein sequences, running BLASTp, and parsing alignment results) |
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第5週 |
10/11 |
Multiple sequence alignment / hierarchical clustering <br>Reading assignment: <br>1. Chen, et al., Incremental Generation of Summarized Clustering Hierarchy for Protein Family Analysis, Bioinformatics, 2004; <br>2. Chen, et al., Exploiting Homogeneity in Protein Sequence Clusters for Construction of Protein Family Hierarchies, Pattern Recognition, 2006. |
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第6週 |
10/18 |
老師出國開會/課程順延一週 |
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第7週 |
10/25 |
Profiles / HMM / clustering / BLASTClust(HW4: protein sequence clustering) |
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第8週 |
11/01 |
Protein families and domains (pfam) / Prediction of functional residues [E1DS] |
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第9週 |
11/08 |
Patterns (HW5: MAGIIC-PRO, and seeMotif) <br>
Reading assignments: <br>
1. Chen-Ming Hsu, Chien-Yu Chen*, Baw-Jhiune Liu, MAGIIC-PRO: Detecting Functional Signatures by Efficient Discovery of Long Patterns in Protein Sequences, Nucleic Acids Research, Vol. 34, Web Server issue, pp. W356-61, 2006. (please download the corrected version) <br>
2. Darby Tien-Hao Chang, Ting-Ying Chien, and Chien-Yu Chen*, seeMotif: exploring and visualizing sequence motifs in 3D structures, Nucleic Acids Research, Vol. 37, Web Server issue, W552-558, 2009.
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第10週 |
11/15 |
校慶停課 |
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第11週 |
11/22 |
Midterm |
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第12週 |
11/29 |
Classification and regression [HW6: PSI-BLAST and feature eatraction] / Prediction of functional residues [E1DS] |
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第13週 |
12/06 |
Profile-based predictions of SSE, disorder, RSA (HW7: SSE prediction [RS126])
Paper reading: Chung-Tsai Su, Chien-Yu Chen*, and Yu-Yen Ou, Protein Disorder Prediction by Condensed PSSM Considering Propensity for Order or Disorder, BMC Bioinformatics, 7:319, 2006. |
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第14週 |
12/13 |
老師出國開會/於次一週補課 |
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第15週 |
12/20 |
[12/20 and 12/22, 1:20~3:10pm] Modeling gene regulatory networks (臺大生科館3A教室)<br>[12/20, 3:30~5:20pm] (臺大生科館327教室) [工具介紹：Rasmol (第一組), Jmol (第二組), Pymol (第三組), Swiss PDB viewer (第四組)] |
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第16週 |
12/27 |
Structure description / structure alignment / protein structure prediction (HW8: TM-align) |
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第17週 |
01/03 |
Scoring functions / structure alignment / structure modeling (HW9: I-TASSER and TM-align) |
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第18週 |
01/10 |
Docking and molecular dynamics [proposal presentation] |
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第19週 |
01/17 |
Demo of final project |
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