Understanding protein structure is essential for researchers in molecular biology, bioinformatics, and structural biology, as it underpins insights into function, interaction, and disease mechanisms. This two-day training is designed for early-career researchers, PhD students, and postdocs who are new to protein structure analysis. Participants will gain hands-on experience with key tools and databases, including ChimeraX, AlphaFoldDB, as well as MutateX and PROSS, to visualize, explore, compare with the first two tools and design new protein structures with the latter two. The course also introduces structure prediction methods using both online platforms (AlphaFold3, Chai-1) and our local VSC infrastructure (AlphaFold2, Boltz-1). Furthermore, we will use AlphaPulldown, a Python package that streamlines protein-protein interaction screens. On the second day, participants will apply these tools to their own research questions, with guided support. By the end of the training, attendees will be equipped to independently access, analyze, and interpret protein structural data using state-of-the-art resources.