This two-day training session will provide the basics of protein structure analysis and how this information is stored in databases.

On the two days, we will explore and search in online databases containing protein structure information including models from AlphaFoldDB. Furthermore, we will visualize protein structures using Chimera. Different hands-on exercises will allow you to compare the structure of homologues. We will use (online) tools to quantify various interactions in the structures.

We will use AlphaFold2 via the HPC cluster at the VSC UGhent to predict structural models of proteins. An overview of different protein folding predictors is discussed, such as ESMFold, OpenFold and RoseTTaFold.

In the afternoon, the second day is dedicated to your own research question you might want to address via structural predictions using AlphaFold2. Additionally, we will learn to use AlphaPulldown, a Python package that streamlines protein-protein interaction screens.