We describe a method for automated domain discovery for topological profile searches in protein
structures. The method is used in a system TOPStructure for fast prediction of CATH classification
for protein structures (given as PDB files). It is important for profile searches in multi-domain
proteins, for which the profile method by itself tends to perform poorly. We also present an
O(C(n)k +nk2) time algorithm for this problem, compared to the O(C(n)k +(nk)2) time used by
a trivial algorithm (where n is the length of the structure, k is the number of profiles and C(n) is the
time needed to check for a presence of a given motif in a structure of length n). This method has
been developed and is currently used for TOPS representations of protein structures and prediction
of CATH classification, but may be applied to other graph-based representations of protein or RNA
structures and/or other prediction problems. A protein structure prediction system incorporating
the domain discovery method is available at http://bioinf.mii.lu.lv/tops/
