Motivation: Circular permutation is an important type of protein
rearrangement. Natural circular permutations have implications for
protein function, stability, and evolution. Artificial circular permutations
have also been used for protein studies. However, such relationships
are difficult to detect for many sequence and structure comparison
algorithms and require special consideration.
Results: We developed a new algorithm, called Combinatorial Extension
for Circular Permutations (CE-CP), which allows the structural
comparison of circularly permuted proteins. CE-CP was designed to
be user friendly and is integrated into the RCSB Protein Data Bank.
It was tested on two collections of circularly permuted proteins. Pairwise
alignments can be visualized both in a desktop application or
on the web using Jmol and exported to other programs in a variety of
formats.
Availability: The CE-CP algorithm can be accessed through
the RCSB website at http://www.rcsb.org/pdb/workbench/
workbench.do. Source code is available under the LGPL 2.1 as
part of BioJava 3 (http://biojava.org; http://github.com/
biojava/biojava).

http://bioinformatics.oxfordjournals.org/content/early/2014/12/11/bioinformatics.btu823.full.pdf