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Bioinformatics Advance Access published online on March 1, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti331
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received July 23, 2004
Revised February 4, 2005
Accepted February 14, 2005

Applications note

Protein structure topological comparison, discovery, and matching service

G. M. Torrance 1*, D. R. Gilbert 1, I. Michalopoulos 2, and D. W. Westhead 2

1 Bioinformatics Research Centre, Department of Computer Science, University of Glasgow, Glasgow, G12 8QQ, UK
2 School of Biochemistry and Microbiology, University of Leeds, Leeds, LS2 9JT, UK

* To whom correspondence should be addressed.
G. M. Torrance, E-mail: tops{at}brc.dcs.gla.ac.uk


  Abstract

Summary: We describe a fold level fast protein comparison and motif matching facility based on the TOPS representation of structure. This provides an update to a previous service at the EBI, with a better graph matching with faster results and visualization of both the structures being compared against and the common pattern of each with the target domain.

Availability: Web service at http://balabio.dcs.gla.ac.uk/tops or via the main TOPS site at http://www.tops.leeds.ac.uk. Software is also available for download from these sites.


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