Check out:

• The protein folding game foldit. Download and install on your computer, play the introductory puzzles.
• The molecular viewer PyMOL. This tutorial may be helpful in getting started.
• Register for a license key for the program MODELLER.

Useful links:

• The PDB, the repository of experimentally determined protein structures.
• NCBI PSI-Blast.
• MUSCLE protein multiple sequence alignment server.
• PredictProtein protein sequence analysis web server: secondary structure prediction, coiled-coils, transmembrane helices, fold recognition, ...
• PROSITE protein sequence patterns.
• SCOP structure classification database.
• matrix2png, a handy bioinformatics tool.
• Bioinfo MetaServer, consensus fold recognition server.