Holiday
LS II生二220 R5R6R7
The course confers the basic knowledge of Computational Biology at the molecular level. Algorithms and theories taught are applied to analyze DNA/RNA/Protein sequences, bimolecular structures and protein dynamics. Through the course, students learn how basic knowledges in math, physics, chemistry and computation can pave the way to solve mysteries in life at its smallest scale.
Course keywords: Sequence Alignment, Structural Comparison, Protein Dynamics, Machine Learning, Programming WORKSHOP on Programming --> TIME & Location: Every Thurs afternoon R5R6R7 @ R220, LSII, NTHU The workshop teaches you basics about Matlab (or python), 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 Normal Mode Analysis I [Matlab drill] Normal Mode Analysis II - Elastic Network Model [Matlab drill] VI. Evaluation Quizzes (20%) Homework (80%) (highest scored 5 out of >=8 homework) VII. AI Policy/使用規則 - 有條件開放,請註明如何使用生成式AI於課程產出 Conditionally open; please specify how generative AI will be used in course output
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