Here are three bioinformatics tools for protein structure prediction, presented without context or comparison and primarily so I don't forget they exist:
- HHpred. Handy,
fast, and the output is data-rich.
- RaptorX. Will do structure alignments and binding predictions, too. Servers may be sluggish sometimes.
- 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.