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301186 VO Structural Bioinformatics II (2020S)

3.00 ECTS (2.00 SWS), SPL 30 - Biologie

Registration/Deregistration

Details

Language: English

Examination dates

Lecturers

Classes (iCal) - next class is marked with N

preliminary meeting: 3.April 2020, 11.00 -12.00 Uhr
PC-Raum/Strukturbiologie, Viennabiocenter 5,1030 Wien.

Lectures in June from 10.00 - 12.00 and 13.00 - 15.00h
June 8 10-17
June 9 10-17
June 10 10-17
June 11 10-17
June 12 10-17

Monday 08.06. 10:00 - 17:00 STB/EDV-Raum Campus Vienna Biocenter, 1030 Wien
Tuesday 09.06. 10:00 - 17:00 STB/EDV-Raum Campus Vienna Biocenter, 1030 Wien
Wednesday 10.06. 10:00 - 17:00 STB/EDV-Raum Campus Vienna Biocenter, 1030 Wien
Thursday 11.06. 10:00 - 17:00 STB/EDV-Raum Campus Vienna Biocenter, 1030 Wien
Friday 12.06. 10:00 - 17:00 STB/EDV-Raum Campus Vienna Biocenter, 1030 Wien

Information

Aims, contents and method of the course

Aims: The students are expected to be able to use online tools to predict various features of protein structure. They must understand how prediction performance is assessed quantitatively. They must be able to scan and browse the most important databases. They must also be able to refine a protein three-dimensional model through molecular mechanics.
Contents: Theoretical aspects of protein structure prediction methods are presented, including: secondary structure, conformational disorder, coiled-coils, tertiary structure – via homology modelling and threading – quaternary structure. Several exercises are performed by using freely distributed software or online services. The principal databases (PDB, CATH, SCOP, ModiDB, DisProt, ModBase) are described and the procedures to browse/scan then at a professional levels are presented though several small exercises. Molecular mechanics is described and used in three-dimensional model refinement. Introductory information on molecular mechanics and artificial intelligence is provided at the end of the course. Note that student with insufficient physico-chemical background may ask for a private meeting with the lecturer to try to overcome their problems.
Methods: The course will consist in a mixture of lectures and exercises. A structure list of exercises is provided to the student who can solve them home.

Assessment and permitted materials

The students will have an oral examination with two main questions, which covers a chapter of the course (for example modeling, computational docking, performance validation etc.) and a small scanning/browsing exercises of the Protein Data Bank.

Minimum requirements and assessment criteria

At least 70% of the exercises in the class room must be attended.
First question = 40 points
Second question = 40 points
Databse browsing/scanning = 20 points

Examination topics

Protein secondary structure prediction
Protein conformational disorder prediction
Protein tertiary structure prediction
Protein quaternary structure prediction
Protein structure refinement
Databases (PDB, CATH, SCOP, ModiDB, DisProt, ModBase)
Introductory notion on molecular dynamics; artificial neural networks; support vector machines

Reading list

M. M. Gromiha. Protein Bioinformatics, Academic Press, 2010
F. Pazos, M. Chagoyen, Practical Protein Bioinformatics, Springer;

Association in the course directory

MMB II-2, MMB W-2, MGE III-2, MMEI III, M-WZB, PhD MB 1

Last modified: Mo 19.10.2020 14:10