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

Upon successful completion of the module the students are able to:
- Understand and reflect in-depth important concepts of structural bioinformatics (protein structure visualization, secondary structure assignment, tertiary structure assignment, quality of protein structure data, structure databases, structure comparison, structural domains, signal peptides, intra protein contacts, structure function relationship
- practically apply selected methods of structural bioinformatics (e.g. structure databases, structure comparison, protein folding, secondary structure prediction, ab initio 3D structure prediction, homology modelling, threading), and lecture these in form of a presentation to an audience
- be responsive to questions and discussion points regarding their presentation
- take part in a discussion regarding a presentation

Suggested pre-requisites for participation is solid knowledge in bioinformatics, good background knowledge in biology e.g. acquired during the first semester courses of a bioinformatics study.

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. Groups of 2-3 students or each student, depending on the number of attendants, are expected to prepare a presentation about a scientific publication covering an already discussed topic from the lecture. Students that are not involved in the current presentation prepare questions on the topic. In the ensuing group discussion with the supervisor the results and the typical mistakes are discussed.

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

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

The module test involves a written exam and an exercise. The goal of the written exam (90 minutes) is to assess how well the students understand the basic concepts and methods of protein structure analysis and prediction, like 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, and how well they are able to reproduce them under time pressure. 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.
The exercise, which takes place as seminar, is designed to assess to which extent the students can use and understand the methods used for protein structure analysis or prediction, e.g. 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, and take part in discussions on presentations of other students or answer questions on their presentation. The exercise supervisor gives grades for the presentation and the participation in the ensuing discussion. Each student gives at least a part of the whole presentation, which allows the supervisor to assess the performance of students individually and provide points. The course achievement is accepted if students have held the seminar and obtained at least 50% of the total possible number of points. To take part in the exam, the students have to fulfill the course achievement at least once. To pass the module at least the score 4.0 is required.