894308 Modelling and simulation of biomolecules

Lecture and exercise
Semester hours
Lecturer (assistant)
Liu, Jakob , Petrov, Drazen , Oostenbrink, Chris , Poliak, Peter
Offered in
Sommersemester 2023
Languages of instruction


This elective course will discuss computational approaches to model and simulate the structure and dynamics of complex biomolecular systems. The overwhelming amount of sequential and structural data that is currently available, give computational scientists the opportunity to gain insight into the structure and function of proteins and nucleic acids at an atomic resolution. From this, experimental data may be rationalized and subsequently predictions may be made.

Lectures will discuss:
•Description of molecular systems in a computer. Energy calculations using force fields
•Experimental structure determination (X-ray crystallography, NMR) and the corresponding modeling components.
•Statistical ensembles as representation of large numbers of molecules and simulation techniques
•Spatial and thermodynamic boundary conditions in simulations
•Analysis of simulations to compare to experimental data; prediction of molecular properties from simulation
•Calculation of free energy differences from molecular simulation
•Conformational sampling and computational tricks and tools to obtain different protein structures more efficiently

For the practical exercises, realistic examples will be provided and a miniature research project will be performed. For the latter, students are encouraged to define their own research questions. Note that the room reservations for the practical exercises are meant to ensure that the room is available, and to offer time to do the practical exercises. The presence of the students it not required during these hours.

Objective (expected results of study and acquired competences)

The aim of the course is to gain insight and experience in modern simulation techniques, applied to biomolecular systems. The course will consist of lectures and practical exercises.
You can find more details like the schedule or information about exams on the course-page in BOKUonline.