However, because updates to the atlas require significant effort, we anticipate that there will always be a time lag between structures arriving in the PDB and cartoons being put into the atlas. In this case users will be able to use the server to generate their own cartoons for the new structures. The software used in the generation of the atlas will be made available in some form, and details will be posted on the WEB site. We have developed a system which supports fast pattern searching over TOPS protein topology databases. The search engine is based on a string-graph algorithm and uses constraint propagation to prune the search space.
Users can search on motifs from a library or define their own search patterns.
A note on TOPS diagrams and patterns A TOPS diagram describes more information about a structure than the corresponding cartoon. In addition to the Secondary Structure Elements - their type, position on the backbone, and orientation relative to the plane of the page. There are two right-handed chirality connections, between strands 1 and 4, and between strands 6 and 8 respectively. This is achieved by permitting insertions of some SSEs into the pattern to obtain a diagram. Each backbone connection between every pair of SSEs is annotated with a pair of integers standing for the minimum and maximum number of SSEs which can be inserted.