Combinatorial Extension (CE)

A method for comparing and aligning protein structures

This page is intended as a pointer to get you to the most recent information on CE and to enable you to perform the calculations you need. CE is now an integral part of the RCSB Protein Data Bank (PDB) and continues to be developed in the Bourne laboratory as needed.

Key Pointers

What follows is a brief description of the history of CE and some additional references and pointers.


  • 1998 - CE method released and original paper published [1]
  • 2000 - CE used to map existing protein fold space [2]
  • 2001 - Pairwise alignment database made available [3]
  • 2004 - A parallel version of CE was developed [4] (no longer relevant)
  • 2004 - A multi-structure version of CE was released CE-MC [5]
  • 2005 - A benchmark dataset of hand alignments was computed and run against CE [6]
  • 2010 - Precalculated CE alignments and a pairwise alignment server made available from the RCSB PDB [7]
  • 2010 - Code modified to handle circular permutations (to be published).
  • 2012 - Precalculated alignments at RCSB PDB site are now based on SCOP and PDP domain assignments.
  • 2013 - Improvements for database searches

Other pointers


[1] Protein Structure Alignment by Incremental Combinatorial Extension of the Optimum Path.
I.N. Shindyalov and P.E. Bourne
Protein Engineering 1998, 11(9) 739-747.
[2] An Alternative View of Protein Fold Space.
I.N. Shindyalov and P.E. Bourne
2000 Proteins: Structure, Function and Genetics 38(3), 247-260.
[3] CE: A Resource to Compute and Review 3-D Protein Structure Alignments.
I.N. Shindyalov and P.E.Bourne
2001 Nucleic Acid Research, 29(1) 228-229.
[4] High Throughput Biological Data Processing on Massively Parallel Computers.
A Case Study of Pairwise Structure Comparison and Alignment Using the Combinatorial Extension (CE) Algorithm.
D. Pekurovsky, I.N. Shindyalov, P.E. Bourne
2004 Bioinformatics, 20(12) 1940-1947
[5] CE-MC: A multiple protein structure alignment server.
C. Guda, S. Lu, E.D. Scheeff, P.E. Bourne and I.N. Shindyalov
2004 Nucleic Acids Research, 32 W100-W103.
[6] Structural Evolution of the Protein Kinase-Like Superfamily
E. Scheeff and P.E. Bourne
2005 PLoS Comp. Biol. 1(5): e49.
[open access] [Video]
[7] Precalculated Protein Structure Alignments at the RCSB PDB website.
A. Prlic, S. Bliven, P.W. Rose, W.F. Bluhm, C. Bizon, A.Godzik, P.E. Bourne
2010  Bioinformatics 10.1093/bioinformatics/btq572.


The original CE method was developed by Ilya Shindyalov and Philip Bourne.
CE-MC was developed be C. Guda and Eric Scheeff in collaboration with the CE authors.
The Java version of CE (jCE) was developed by Andreas Prlic.
The addition of support to handle circular permutations was developed by Spencer Bliven and Andreas Prlic.