Detection of circular permutations within protein structures using CE-CP

Bioinformatics. 2015 Apr 15;31(8):1316-8. doi: 10.1093/bioinformatics/btu823. Epub 2014 Dec 12.


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 and implementation: The CE-CP algorithm can be accessed through the RCSB website at Source code is available under the LGPL 2.1 as part of BioJava 3 (;

Contact: or

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Databases, Protein*
  • Dynamins / chemistry*
  • Humans
  • Programming Languages
  • Protein Structure, Tertiary
  • Sequence Analysis, Protein / methods
  • Structural Homology, Protein*


  • Dynamins