Universität Wien FIND

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301186 VO Structural Bioinformatics II (2021S)

3.00 ECTS (2.00 SWS), SPL 30 - Biologie
GEMISCHT

An/Abmeldung

Hinweis: Ihr Anmeldezeitpunkt innerhalb der Frist hat keine Auswirkungen auf die Platzvergabe (kein "first come, first served").

Details

Sprache: Englisch

Prüfungstermine

Lehrende

Termine

-vor Ort Lehre oder hybrid -
Preliminary Meeting: 26.03. 2021, 17-18 Uhr
- SR/VBC 5 Strukturbiologie
Termine:
Lectures (PC room, Dept. Struct. Comput. Biol.)
May 17: 10-12 and 13-16
May 18: 10-12 and 13-16
May 19: 10-12 and 13-16
May 20: 10-12 and 13-16
May 21: 10-12 and 13-16

Exams
Appointment


Information

Ziele, Inhalte und Methode der Lehrveranstaltung

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.

Art der Leistungskontrolle und erlaubte Hilfsmittel

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.

Mindestanforderungen und Beurteilungsmaßstab

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

Prüfungsstoff

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

Literatur

M. M. Gromiha. Protein Bioinformatics, Academic Press, 2010
F. Pazos, M. Chagoyen, Practical Protein Bioinformatics, Springer;
2015

Zuordnung im Vorlesungsverzeichnis

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

Letzte Änderung: Mi 30.06.2021 10:09