301186 VO Structural Bioinformatics II (2024S)
Labels
Registration/Deregistration
Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).
Details
Language: English
Lecturers
Classes (iCal) - next class is marked with N
10.00 - 12.00 und 13.00 - 15.00 Uhr
CCR03 (VBC5/1.113), Viennabiocenter 5,1030 Wien.
N
Monday
10.06.
10:00 - 15:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Tuesday
11.06.
10:00 - 15:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Wednesday
12.06.
10:00 - 15:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Thursday
13.06.
10:00 - 15:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Friday
14.06.
10:00 - 15:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Information
Aims, contents and method of the course
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
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
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;
F. Pazos, M. Chagoyen, Practical Protein Bioinformatics, Springer;
Association in the course directory
MMB III-1a:, MMB II-2, PhD MB
Last modified: Mo 15.04.2024 09:46
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.