Here are three bioinformatics tools for protein structure prediction, presented without context or comparison and primarily so I don't forget they exist:

  1. HHpred. Handy, fast, and the output is data-rich. 
  2. RaptorX. Will do structure alignments and binding predictions, too. Servers may be sluggish sometimes.
  3. I-TASSER. They've added some neat functional prediction modules (primarily based on existing structures and GO terms, I think) since I've last used the server.