FAST is a new algorithm for aligning three-dimensional structures of proteins. FAST employs an elimination heuristic to quickly and reliably detect the global optimum residue-residue alignment. The main application is detection of structural and functional similarities that are not available with traditional sequence alignment algorithms. FAST can be run from the web by uploading two PDB files in the form below. You can also download the executable for offline use.

Reference:
Zhu J and Weng Z, FAST: A Novel Protein Structure Alignment Algorithm, Proteins: Structure, Function and Bioinformatics (2005) Vol 14, 417-423.