OSAKA UNIV. CBCMP

OSAKA UNIVERSITY CHEMISTRY - BIOLOGY COMBINED MAJOR PROGRAM

Bioinformatics

Outline

This course is heavily tilted toward Structural Bioinformatics. Students will learn the fundamental concepts and methods for structural bioinformatics and their applications. Students will be expected to understand the concepts taught and obtain practical abilities, with the objective to help students to use structural bioinformatics tools/methods to solve problems in their future research.

Learning outcomes

By the end of the course, students are expected to be able to:

1. Describe the structures of protein, DNA, and RNA

2. Explain the relationship between protein sequence and protein structure

3. Describe how structure translates into various biological functions such as catalysis, transport, and regulation

4. Explain the basic principles of experimental methods for the determination of the structure of macromolecules

5. Use sequence and structural databases and extract useful information from them

6. Use computer programs to visualize three-dimensional structures and analyze the relationship between structure and function

7. Know how to check and confirm the validity of information in structural databases

8 Use bioinformatics tools for sequence alignment, sequence motif identification and prediction of secondary and tertiary structures

9. Understand for the purpose, theoretical background and limitations of the aforementioned bioinformatics methods and use this knowledge to interpret relevant results

10 Know how to perform molecular dynamics simulation for a given macromolecular structure to assist and/or explain data from wet experiment.

Textbook

Reference textbooks:

Bourne PE. & Weissig H. (eds) 2003. Structural Bioinformatics (Methods of Biochemical Analysis, V. 44). Wiley-Liss, USA. ISBN: 0471201995

 

Koča, J., Svobodová Vařeková, R., Pravda, L., Berka, K., Geidl, S., Sehnal, D., Otyepka, M. (2017) Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases (SpringerBriefs in Biochemistry and Molecular Biology). Springer USA. ISBN: 3319473875

Syllabus

Module 1:  Introduction, fundamentals of biomolecular structures

Module 2: Principles of x-ray crystallography, NMR, and electron microscopy

Module 3: Computational aspects of crystallographic macromolecular structure determination

Module 4: Molecular visualization

Module 5: Structure validation and quality assurance

Module 6: The Protein Data Bank and the PDB format of macromolecular models

Module 7: Protein structure evolution and the SCOP database

Exam1

Module 8: Structure comparison and alignment

Module 9: Identifying structural domains in proteins

Module 10: Inferring protein function from structure

Module 11: Protein-protein interaction with antigen recognition by antibodies

Module 12: Principles and methods for docking and ligand design

Module 13: Structural bioinformatics in biological and chemical drug discovery

Module 14: Homology and ab initio modeling

Exam 2

Grading

Assessment

Criteria

Bioinformatics

(2 credits)

Bioinformatics

Exercise Session (2 credits)

Attendance

5%

5%

Examinations (2)

80%

-

Quiz, homework, assignment

-

80%

Class participation

15%

15%

Instructor

Associate Professor

Clement Angkawidjaja

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