752312 From sequence to structure: prediction, modeling and molecular dynamics of protein structures

Lecture and exercise
Semester hours
Lecturer (assistant)
Leitner, Christian , Ludwig, Roland
Institute of Food Technology
Offered in
Sommersemester 2018
Languages of instruction


Each morning the course starts with the theoretical background necessary to perform the practical work in the afternoon. Lectures and discussions will frequently change in the theoretical sessions. Topics covered by the lectures and practical exercises:

1) Prediction of the secondary structure starting with amino acid sequences
* Multiple sequence alignments (ClustalX, T-Coffee, Muscle)
* Phylogenetic analysis (MEGA 5)
* Web based sequence analyzing tools (available through the SwissProt server)
2) Modeling of proteins
* Preparing homology models of proteins (SwissModel)
* Visualisation and manipulation of protein structures (DeepView, PyMOL)
3) Force field calculations, energy minimization, simple molecular dynamic
* Docking experiments (Autodock, ZINC database)
* Molecular dynamics simulation (Tinker with Force Field Explorer, GROMACS)

Objective (expected results of study and acquired competences)

The knowledge of the quaternary structure of proteins is important for the understanding of their function. Currently, the more than 120,000 available protein structures (solved by X-ray structure analysis or NMR), form only a small fraction of all known protein sequences. Since protein structure determination is still a time consuming and expensive process, methods for predicting unknown structures were developed. The goal of this course is to demonstrate such methods to the students by theory and practical work. The course will include the prediction of secondary structures starting from the amino acid sequence, building a model of an unknown protein by using a "template" (a closely related protein with an already solved structure) and the introduction to docking simulations. Students will perform these tasks during the practical computer based excercises. The used computer programs are free of charge for nonprofit organizations.

At the end of the course you will be able to:
* choose the most suitable template for homology modelling
* evaluate and check the generated/predicted model structures
* consider the strenghts and weaknesses of applied methods
* evaluate which method will provide the best result

Additionally, a better knowledge of the structure-function relationship in proteins will be developed.
You can find more details like the schedule or information about exams on the course-page in BOKUonline.