Structural Bioinformatics

The following topics are core elements of the module:
- protein structure visualization
- secondary structure assignment
- tertiary structure assignment
- quality of protein structure data
- structure databases
- structure comparison
- structural domains
- protein folding
- secondary structure prediction
- ab initio 3D structure prediction
- homology modelling
- threading
- signal peptides
- intra protein contacts
- structure function relationship

The following topics are core elements of the module:
- protein structure visualization
- secondary structure assignment
- tertiary structure assignment
- quality of protein structure data
- structure databases
- structure comparison
- structural domains
- protein folding
- secondary structure prediction
- ab initio 3D structure prediction
- homology modelling
- threading
- signal peptides
- intra protein contacts
- structure function relationship

Grundkenntnisse in der Bioinformatik (Sequenzanalyse, molekulare Evolution)
Grundkenntnisse in der Zellbiologie/Biochemie
Grundkenntnisse in der Statistik

The selected teaching approach Lecture course and the selected teaching method Oral talk are especially well suited for imparting basic concepts, methodological approaches as well as typical problems of structural bioinformatics to students with basic knowledge of bioinformatics. In particular the exercise serves as a way to deepen the learning content of the lecture. The students are expected to prepare a scientific publication covering an already discussed topic from the lecture. In the exercise the algorithms and methods used in the publication are discussed. Where possible, the usage of the methods and the analysis of selected case studies from the publication is presented in class. Thus, also the application of the methods is trained. It will be announced before each exercise which scientific publication will be discussed. The students are encouraged to prepare the contents of the paper and familiarize their selves with the methods used. The lecturer discusses the procedures and methods in the exercise, and responds to questions and problems. Where possible, small selected case studies are solved together in the exercise, or are presented by students.

Scientific publications, presentation of slides, discussions during lectures, materials on the module Web page.age.

- Bourne & Weissig, Structural Bioinformatics
- Understanding Bioinformatics, M. Zvelebil and J.O.Baum, Garland Science 2008

The module test involves a graded written exam.
The goal of the written exam (90 minutes) is to assess how well the students understand the basic concepts of protein structure analysis and prediction (like protein structure visualization, secondary structure assignment, tertiary structure assignment, quality of protein structure data, structural domains, signal peptides, intra protein contacts, structure function relationship) and how well they are able to reproduce them in limited time. Based on exemplary method calls, interrogation of input and output of methods, as well as the building of possible method pipelines to solve a specific bioinformatics problem, and the interpretation of method results, it is assessed how well the students are able to do bioinformatics analyses on their own, choose appropriate methods suitable to a specific problem and apply these. No electronic devices are allowed except for pocket calculators. Students are asked to write free-text answers to questions, solve algorithmic and logical problems, and to work through a limited number of multiple-choice questions by ticking the right answer.

To pass the module at least the score 4.0 is required.