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Nucleic Acids Research, 2004, Vol. 32, Database issue D251-D254
© 2004 Oxford University Press

TOPS: an enhanced database of protein structural topology

Ioannis Michalopoulos, Gilleain M. Torrance1, David R. Gilbert1 and David R. Westhead*

School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK and 1 Department of Computing Science, University of Glasgow, 17 Lilybank Gardens, Glasgow G12 8QQ, UK

*To whom correspondence should be addressed. Tel: +44 113 343 3116; Fax: +44 113 343 3167; Email: d.r.westhead{at}leeds.ac.uk

The TOPS database holds topological descriptions of protein structures. These compact and highly abstract descriptions reduce the protein fold to a sequence of Secondary Structure Elements (SSEs) and three sets of pairwise relationships between them, hydrogen bonds relating parallel and anti- parallel ß strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in ß{alpha}ß units and between parallel {alpha} helices. The database is used as a resource for visualizing folding topologies, fast topological pattern searching and structure comparison. Here, significant enhancements to the TOPS database are described. The topological description has been enhanced to include packing relationships between helices, which significantly improves the description of protein folds with little ß strand content. Further, the topological description has been annotated with sequence information. The query interfaces to the database have been improved and the new version can be found at http://www.tops.leeds.ac.uk/.


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