Above the logo area (name of site and description etc) is the main page link menu with a multi level drop down menu for categories underneath this section.
The theme also uses image thumbnails for listing posts on the home page and in categories. At the bottom of the site is space for 4 footer widgets.
Prototype is free to download however those who join the Theme Hybrid Theme Club will gain access to tutorials, documentation and the support forum.
If you are looking for something minimal or something basic to modify yourself, I recommend checking it out.