301185 VO Structural Bioinformatics I (2023W)
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ON-SITE
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
Examination dates
Lecturers
Classes (iCal) - next class is marked with N
Module examination
The oral exam will be given in English and will be scheduled with the course coordinator once the course has ended. It is kept individually on-site (but it might be kept digitally if necessary).The test is divided into three sections: a subject chosen by the examiner, a topic chosen by the student, and a molecular graphics exercise using PyMol or Chimera on the professor's computer. Databases of protein domains and comparisons of protein structures are two examples of subjects. Examples of molecular graphics tasks include identifying beta-sheets, figuring out if a residue is solvent accessible, identifying disulfide bonds, and characterizing metal biosites.The students must demonstrate that they have a firm grasp of the exam's topics and be able to outline their approach to solving a molecular graphic issue.
Monday
15.01.
10:00 - 16:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Tuesday
16.01.
10:00 - 16:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Wednesday
17.01.
10:00 - 16:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Thursday
18.01.
10:00 - 16:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Friday
19.01.
10:00 - 16:00
CCR03-Raum 1.113 Campus Vienna Biocenter, 1030 Wien
Information
Aims, contents and method of the course
Programme Introduction to the molecular graphics and analysis of the most common protein folds with RasMol, Pymol and Chimera. Measurements of structural similarity between proteins, theory and applications (Dalilite, CE, PDBeFold and other tools). Databases of macromolecular structures: the Protein Data Bank, the wwPDB and the ePDB. Databases of structural domains: CATH, SCOP, and SCOP2. Databases of protein domains: Pfam, InterPro, InterProScan. Databases of computational models: ModBase and BioModels. Validation of experimental macromolecular structures. The problem of data redundancy.
Assessment and permitted materials
Oral exam
Minimum requirements and assessment criteria
The student must be able to compare two protein three-dimensional structures, be aware of the most important biological databases, and be able to solve basic exercises of molecular graphics.
Examination topics
Here is a list of specific topics: Superposition, rmsd, m-score, TM-score, techniques of superposition, basic database theory, PDB, CATH, SCOP, ModBase, DisProt, MobiDB, representativeness and redundancy, PISCES, PDBselect.
Reading list
Association in the course directory
MMB II-2, MMB W-2, MMB III-1a.,MGE III-2, MMEI III, UF MA BU 01, UF MA BU 04
Last modified: Th 21.03.2024 10:46