TOPS: An enhanced database of protein structural topology

Abstract

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 β strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in βαβ units and between parallel α 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 β strand content. Further, the topological description has been annotated with sequence information. The query interfaces to the database have been proved and the new version can be found at http://www.tops.leeds.ac.uk/.