Bioinformatics, Vol 15, 317-326, Copyright © 1999 by Oxford University Press
D Gilbert, D Westhead, N Nagano and J Thornton
MOTIVATION: TOPS cartoons are a schematic ion of protein three- dimensional
structures in two dimensions, and are used for understanding and manual
comparison of protein folds. Recently, an algorithm that produces the
cartoons automatically from protein structures has been devised and
cartoons have been generated to represent all the structures in the
structural databank. 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 tested
on a database derived from all the current entries in the Protein Data Bank
(15,000 domains). Users can search on patterns selected from a library of
motifs or, alternatively, they can define their own search patterns.
AVAILABILITY: The system is accessible over the Web at
http://tops.ebi.ac.uk/tops
ARTICLES
Motif-based searching in TOPS protein topology databases
Department of Computer Science, City University, London EC1V 0HB, UK. drg@cs.city.ac.uk
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