Nucleic Acids Research Advance Access originally published online on May 22, 2009
Nucleic Acids Research 2009 37(Web Server issue):W539-W544; doi:10.1093/nar/gkp411
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W539-W544
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
COPS—a novel workbench for explorations in fold space
Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
*To whom correspondence should be addressed. Tel: +43 662 8044 5796; Fax: +43 662 8044 176; Email: sippl{at}came.sbg.ac.at
Received February 23, 2009. Revised April 23, 2009. Accepted May 2, 2009.
The COPS (Classification Of Protein Structures) web server provides access to the complete repertoire of known protein structures and protein structural domains. The COPS classification encodes pairwise structural similarities as quantified metric relationships. The resulting metrical structure is mapped to a hierarchical tree, which is largely equivalent to the structure of a file browser. Exploiting this relationship we implemented the Fold Space Navigator, a tool that makes navigation in fold space as convenient as browsing through a file system. Moreover, pairwise structural similarities among the domains can be visualized and inspected instantaneously. COPS is updated weekly and stays concurrent with the PDB repository. The server also exposes the COPS classification pipeline. Newly determined structures uploaded to the server are chopped into domains, the locations of the new domains in the classification tree are determined, and their neighborhood can be immediately explored through the Fold Space Navigator. The COPS web server is accessible at http://cops.services.came.sbg.ac.at/.