jCE/jFATCAT 20150427 – Calculate Structure Alignment

jCE/jFATCAT 20150427


CE (Combinatorial Extension) 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.


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

jFatCat is a re-implementation of the FATCAT algorithm in the Java programming language.


Andreas Prlić(andreas@sdsc.edu) , Philip E. Bourne(bourne@sdsc.edu)




  • Linux/ Windows/ MacOsX
  • Java





Shindyalov IN, Bourne PE (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Engineering 11(9) 739-747.

Precalculated Protein Structure Alignments at the RCSB PDB website
Andreas Prlic; Spencer Bliven; Peter W Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq572

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