TOPS: an enhanced database of protein structural topology.
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 beta strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in betaalphabeta 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 beta 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/.
Michalopoulos
Ioannis
I
School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
Torrance
Gilleain M
GM
Gilbert
David R
DR
Westhead
David R
DR
D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding; D016247:Information Storage and Retrieval; D020407:Internet; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D014584:User-Computer Interface
D011506:Proteins