Protein structure and computational biology

• describe protein structure elements, their properties and the chemical and structural properties of amino acids.
• evaluate the quality of experimental and model structures.
• navigate PDB database and operate with PyMOL for visualisation and analyses of protein structures.
• construct models of a protein of unknown structure and analyze them.
• 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.
• perform molecular simulations to study protein dynamics.
• apply command-line tools on a computing server.

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 with flipped-class, computer exercises, hand-in exercises, group work. In the second part of the course, starting after Lecture7, there will be activities for project to develop in groups which is used for the final exam.

The project work at the end of the course is performed in small, self-elected groups with members from different expertises/background and completed with scientific articles that the students should write themselves and produce data for the results section.

The exercises deal with protein structure visualisation using the program PyMOL. The models will be predicted with AlphaFold. The mutational scans will be performed using FoldX and similar tools on a Linux cluster. For part of the exercises and in the project work, we will work on a Linux Cluster using the terminal and command-line based software.

Minimum: 10, Maximum: 120.

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.