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
-
Class 1: Mainly Alpha
-
Class 2: Mainly Beta
-
Class 3: Mixed Alpha-Beta
-
Class 4: Few Secondary Structures
References
- Holm L & Park J. (2000) DaliLite workbench for
protein structure comparison. Bioinformatics
16:566-567.
- The pairwise DaliLite
server : http://www.ebi.ac.uk/DaliLite/
- 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.
- The ASTRAL
homepage : http://astral.berkeley.edu./
- 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
- The CATH
homepage : http://www.cathdb.info/latest/index.html