Here you may find a nice step-by-step tutorial written by Enrico Perspicace (thanks Enrico!) to install Open3DTOOLS on your system.

Here you may find a basic tutorial to learn using Open3DQSAR and Open3DALIGN.

Here you may download a very comprehensive advanced tutorial (winner of the Teach-Discover-Treat competition 2012) which shows how to use Open3DQSAR and Open3DALIGN in the context of virtual screening.