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

Lecture and exercise
Semester hours
Lecturer (assistant)
Ludwig, Roland
Offered in
Sommersemester 2024
Languages of instruction


The knowledge of the quaternary structure of proteins is important for the understanding of their function. The more than 140,000 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 an amino acid sequence (target sequence), building a model of an unknown protein by using a "template" (a protein with high sequence identity and an already solved structure) and the introduction to docking simulations. Students will perform these tasks in computer based excercises. The used computer programs are free of charge for nonprofit organizations.
The course will be thaught as correspondance course via Zoom. All necessary documents and programs will be made available at BOKUlearn (Moodle) or can be downloaded from the internet. Theoretical and practical lectures will be thaught via Zoom. A second monitor or computer is a great plus for the practical parts of the course.

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, Muscle)
* Phylogenetic analysis (MEGA 10)
* Web based sequence analyzing tools (available through the SwissProt server)
2) Modeling of proteins
* Preparing homology models of proteins (SwissModel, PHYRE2)
* Visualisation and manipulation of protein structures (PyMOL)
3) Force field calculations, energy minimization, simple molecular dynamic
* Docking experiments (Autodock, ZINC database)
* Molecular dynamics simulation (GROMACS)

Objective (expected results of study and acquired competences)

After the positive completion of the course students can:

1) Choose the most suitable template for a target sequence (by phylogenetic analysis with MEGA 10) for homology modeling (SwissModel, PHYRE2)
2) Analyze and examine the generated protein models (by superimposition (PyMol)
3) Compare and contrast the strenghts and weaknesses of the appliede programs and methods (homology modeling, threading,...)
4) Hypothesize which method will provide the best structural models for a target sequence
This course will deepen your knowledge of the structure-function relationship in proteins.
You can find more details like the schedule or information about exams on the course-page in BOKUonline.