CE is a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment. Complete details are described in the paper (PDF format).


jCE is a re-implementation of the original CE source code in the Java programming language. While the algorithm is principle exactly the same as in the original implementation, jCE provides several improvements over the original code:

  • New internal data model: The internal representation of jCE is now based on the BioJava protein structure module. It supports both PDB file and mmCif files as input.
  • User Interface: jCE provides a completely new user interface for easier set up of pairwise alignments and database searches.
  • This 3D alignment program is based on BioJava and Jmol.

Command line arguments

A detailed documentation of the available command line arguments is available.


Measure of the statistical significance of the result relative to an alignment of random structures. Typically proteins with a similar fold will have a Z-score of 3.5 or better. The Z-score can be used to filter less significant results or alternatively look for weak similarities.


jFatCat is a re-implementation of the FATCAT algorithm in the Java programming language. More information is available from the official FATCAT website.