For homology modeling, DeCypher’s BLAST and Smith-Waterman methods are perfect for identifying new sequences with protein structure and comparing them against the Protein Data Bank (PDB). For sequences that do not have significant homology with PDB sequences, DeCypherHMM can be used to identify protein structural families reported in SCOP by comparing them against the Superfamily database.

Reference:

Martin Madera et al., The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res., Jan 2004; 32: 235 - 239.