智慧型機器學習與電腦輔助藥物設計
Intelligent Machine Learning and Computer-aided Drug Design
學期
109-2
學分
3
學分
當期課號
5720
永久課號
IBI5121
開課單位
生物資訊及系統生物研究所
授課教師
楊進木
校區
博愛
類別
選修
上課時間表
| 節 | 週四 |
|---|---|
5 13:20–14:10 | 智慧型機器學習與電腦輔助藥物設計 BI305 3 節連堂 |
6 14:20–15:10 | |
7 15:30–16:20 |
* 根據陽明交大上課時間表所列
概述
Studying the concepts, tools, algorithms, scoring functions of computation systems biology and drug design.
先修科目
None
教學方式
Public databases, tools, and website.
評分方式
Homework (40%) Progress report or paper report Final project (40%) Examination: 20%
週次計畫
| 週次 | 主題 |
|---|---|
| 第 1 週 | Course Outlines |
| 第 2 週 | Introduction to Drug Design & Systems Biolog |
| 第 3 週 | iGEMDOCK: PC run GEMDOCK in Unix and PC-Cluster |
| 第 4 週 | GEMDOCK: Briefly introduction source Assign target proteins |
| 第 5 週 | Introduction to target proteins (All members) Prepare compound databases Compound format convert (OpenBabel) |
| 第 6 週 | Target analysis: Sequence-based analysis MSA (conservation analysis), domain analysis, GO analysis evolutionary tree (MEGA-7) |
| 第 7 週 | Target analysis: Structure-based analysis Prepare binding site、Swisspdbviewer CE, DALI |
| 第 8 週 | Post-screening analysis: Top-rank 500 compounds 1. Compound structure Clustering by (iGEMDOCK) 2. Interaction clustering |
| 第 9 週 | Post-screening analysis: SimMap analysis 1. Anchor analysis 2. Moiety analysis |
| 第 10 週 | Post-screening analysis: clustering and SimMap analysis |
| 第 11 週 | Identify potential compounds: First round Validation by biological functions, conservations, known inhibitors or mechanisms |
| 第 12 週 | Selection potential compounds: 1. Verify compounds by known databases (STITCH, BindingDB) 2. Multiple target analysis |
| 第 13 週 | Selection potential compounds: Omics-based analysis (L1000: genomics protein-ligand analysis |
| 第 14 週 | Report selection compounds to collaborators: First round |
| 第 15 週 | Target protein analysis: Systems Biology Approaches (GEO databases: microarray analysis) |
| 第 16 週 | Target protein analysis: Systems Biology Approaches (cytoscape |
| 第 17 週 | Report selection compounds to collaborators: Second round |
| 第 18 週 | Final project |
教科書
Selected papers for each topics
Office Hours
- 地點
- 賢齊館415-1
- 時間
- 2CD
- 聯絡方式
- 56942