Motif-based searching in TOPS protein topology databases

Motivation: TOPS cartoons are a schematic abstraction of protein three-dime nsional structures in two dimensions, and are used for understanding and ma nual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoon s have been generated to represent all the structures in the structural dat abank. There is now a need to be able to define target topological patterns and to search the database for matching domains. Results: We have devised a formal language for describing TOPS diagrams and patterns, and have designed an efficient algorithm to match a pattern to a set of diagrams. A pattern-matching system has been implemented, and teste d on a database derived from all the current entries in the Protein Data Ba nk (15000 domains). Users can search on patterns selected from a library of motifs or; alternatively, they can define their own search patterns.