WORKSHOP on Programming --> TIME & Location: (TBD) @ R220, LSII

[The workshop teaches you basics about Matlab, Linux and Visualization software
(VMD, Pymol,
Swiss-PDB-Viewer etc)]


I. Course Description
Conferring the basic knowledge of how math and physics have been helping solve
biological
problems

II. Text Books
Molecular Modeling - Principles and Applications, by Andrew R Leach

III. References
"Biochemistry, 5th edition", by Garrett & Grisham. Publisher: Thomson/Brooks/Cole
“Molecular Biophysics”, by Daune
"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids"
Richard Durbin,
Sean R.
Eddy, Anders Krogh, Graeme Mitchison (E-book at NTHU library) or
http://eisc.univalle.edu.co/cursos/web/material/750068/1/6368030-Durbin-Et-Al-
Biological-
Sequence-Analysis-CUP-2002-No-OCR.pdf
“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
Math Chapters (Appendix) in "Quantum Chemistry" by Donald McQuarrie

IV. Teaching Method
Lectures plus after-class hands-on practice in programming and using computer
software

V. 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 Comparison and Prediction I [VMD intro]
Protein Structure Comparison and Prediction II [VMD / tcl script]
Protein Dynamics I - Monte Carlo simulations and small ligand docking
[Matlab/Autodock drill]
Molecular Dynamics Simulations I
Molecular Dynamics Simulations II
Molecular Dynamics Simulations III
Normal Mode Analysis I [Matlab drill]
Normal Mode Analysis II - Elastic Network Model [Matlab drill]
Protein-Nucleotides and Protein-Protein interaction

VI. Evaluation
Quizzes (20%)
Homework (80%) (highest scored 5 out of >=8 homework)