Protein structure and computational biology

• reproduce the 20 natural amino acids and account for their structural and chemical properties.
• describe the basic protein structure elements and their properties.
• describe the main steps for determination of three-dimensional protein structures using NMR spectroscopy and x-ray crystallography, and account for essential strengths and weaknesses of the two methods.
• navigate the PDB structure database and the corresponding file types.
• operate the basic functions of the program PyMOL for visualisation of protein structure.
• construct models of a protein of unknown structure.
• evaluate the quality of experimental and model structures.
• analyse and discuss the structural context of annotated protein features such as epitopes, post-translational modifications and active sites.
• predict the effect of point mutations on the interaction with ligands, conformational changes and other structural properties.
• design and develop a scientific article and learn principles for peer-review.

Protein structure from primary to quaternary, experimental determination of protein structures, structural genomics, prediction of secondary structure, accessibility etc, fold recognition, homology and de novo modelling, structure validation, protein structure analysis, protein engineering, molecular dynamics simulations

22111/22113, Basic knowledge of Bioinformatics and Chemistry

Lectures, computer exercises, hand-in exercises and group work

The project work at the end of the course is performed in small, self-elected groups and completed with scientific articles.

The hand-in exercises (2) deal mainly with protein structure visualisation using the program PyMOL. The models will be predicted with HHPred and AlphaFold2. The mutational scans will be performed using FoldX.

Minimum: 10, Maximum: 70.

Please be aware that this course has a minimum requirement for the number of participants needed, in order for it to be held. If these requirements are not met, then the course will not be held. Furthermore, there is a limited number of seats available. If there are too many applicants, a pool will be created for the remainder of the qualified applicants, and they will be selected at random. You will be informed 8 days before the start of the course, whether you have been allocated a spot.