SCOPExplorer: a tool for browsing and analyzing structural classification of proteins (SCOP) data.
We have developed a tool, named "SCOPExplorer", for browsing and analyzing SCOP information. SCOPExplorer 1) contains a tree-style viewer to display an overview of protein structure data, 2) is able to employ a variety of options to analyze SCOP data statistically, and 3) provides a function to link protein domains to protein data bank (PDB) resources. SCOPExplorer uses an XML-based structural document format, named "SCOPML", derived from the SCOP data. To evaluate SCOPExplorer, proteins containing more than 20 domains were analyzed. The Skp1-Skp2 protein complex and the Fab fragment of IgG2 contain the largest numbers of domains in the current eukaryotic SCOP database. These proteins are known to either bind to various proteins or generate diversity. This suggests that the more domains a protein has, the more interactions or more variability it will be capable of. (SCOPExplorer is available for download at http://scopexplorer.ulsan.ac.kr).
Ahn
Geon-Tae
GT
Department of Biological Science, University of Ulsan, Ulsan 680-749, Korea.
Kim
Jin-Hong
JH
Hwang
Eui-Yoon
EY
Lee
Myung-Joon
MJ
Han
In-Seob
IS
D000818:Animals; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000145:classification*
D011506:Proteins