With the upcoming new release there will be a couple of new protein structure alignment related features:
*) The RCSB PDB web site is providing a structure alignment service. This service can calculate structure alignment on the server side. It also caches all alignments. This means if you come back the next day you can view the same result quickly.
Preview the new alignment service here:
*) Circular Permutations (CP) in proteins are difficult for alignment algorithms to detect since they depend on the sequence order. These permutations are re-arrangements of the sequence, resulting in different amino acid connectivity, while conserving the overall 3D shape of a protein. Spencer Bliven has extended the Java version of CE and introduced support for the detection of such permutations. This is achieved by working with an internal representation of the proteins that allows to identify alignments across N and C termini. Since this slows down the calculation about three times, the detection of CP is optional.
View an Example of a Cirularly Permutated protein structure alignment