301186 VO Structural Bioinformatics II (2024S)

Aims: This five-day course will give an overview of structural bioinformatics and cover a few practical parts of it. The students will be shown how to use online tools in their future study, including BLAST, UniProt, PSIPRED, PDB, PDBsum, IUPred3, ODiNPred, SMART, etc. They will also learn to use a number of start-of-the-art methods for protein structure prediction and analysis, including SWISS-MODEL, ESMFold, RoseTTAFold, AlphaFold etc. Additionally, they will be able to use online servers, such as DoGSiteScorer and FTMap, to predict the druggability of the target proteins of their interest.

Contents: The course will cover the following topics: basics of structure of nucleic acids and proteins, protein structural and functional analysis, structure prediction and validation, structure-based drug discovery, etc. The course will train students to use online tools to retrieve protein/DNA sequences and to predict the folding and 3D structure of proteins. We will move on to learn how to evaluate the druggability of a target protein and further investigate structure-based drug discovery, including high-throughput library screening, virtual screening and fragment-based drug design. In the end, we will together look at a number of real drugs, e.g. aspirin, quinine and dorzolamide, to understand the underlying molecular mechanism of their function.

Methods: The course will consist of both lectures and exercises. The exercises will be demonstrated in the course, but students can continue to practice them at home.