一、課程說明
Course Description Conferring the basic knowledge of how math and physics have been helping solve
biological problems
二、指定用書
Text Books Molecular Modeling - Principles and Applications, by Andrew R Leach
三、參考書籍
References “Molecular Biophysics”, by Daune
"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" Richard Durbin, Sean R.
Eddy, Anders Krogh, Graeme Mitchison
“Structural Bioinformatics” by Jenny Gu, Philip E. Bourne
“Normal Mode Analysis”by Qiang Cui & Ivet Bahar
“Coarse-Graining of Condensed Phase and Biomolecular Systems”by Gregory A Voth
四、教學方式
Teaching Method Lectures plus after-class hands-on practice in programming and using computer
software
五、教學進度
Syllabus

Biological sequences - Nucleic acids and dynamic programming I [Linear Algebra I & Matlab intro I]
Biological sequences - Amino acids and sequence alignment [Linear Algebra II & Matlab intro II]
Probability & Statistics I [Matlab drill]
Probability & Statistics II; Secondary Structure Prediction [Matlab drill]
Protein Structure Prediction I [VMD intro]
Protein Structure Prediction II [VMD / tcl script]
Protein Dynamics I - Monte Carlo simulations [Matlab drill]
Molecular Dynamics Simulations I [NAMD I]
Molecular Dynamics Simulations II [NAMD II]
Molecular Dynamics Simulations III [NAMD III]
Normal Mode Analysis I [Matlab drill]
Normal Mode Analysis II - Elastic Network Model [Matlab drill]
Protein-Protein interaction

六、成績考核
Quizzes (30%)
Homework (70%) (>= 6 homework)