Examples are provided with ComSubstruct and the pairwise DaliLite server [1,2],
where the ASTRAL dataset (1.71 95%) [3,4] is searched by

ComSubstruct  -l  [-v]  -o1  -s  -w1.1    key_sequence.code   target_ASTRAL.code

In the following, protein domain structures from the CATH database [5,6] are used as key protein.

*The program was run on a notebook compuer with 2 GHz Intel Core 2 Duo and 1GB 667 MHz DDR2 SDRAM.

Results of ASTRAL dataset search by ComSubstruct  

  1.   Class 1: Mainly Alpha

  2.   Class 2: Mainly Beta

  3.   Class 3: Mixed Alpha-Beta

  4.   Class 4: Few Secondary Structures

  1. Holm L & Park J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16:566-567.
  2. The pairwise DaliLite server : http://www.ebi.ac.uk/DaliLite/
  3. Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, & Brenner SE. (2004) The ASTRAL compendium in 2004. Nucleic Acids Research 32:D189-D192.
  4. The ASTRAL homepage : http://astral.berkeley.edu./
  5. Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, &  Orengo C. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
    Nucleic Acids Research 33: Database Issue D247-D251
  6. The CATH homepage : http://www.cathdb.info/latest/index.html