Please use this identifier to cite or link to this item: http://buratest.brunel.ac.uk/handle/2438/3024
Title: Domain discovery method for topological profile searches in protein structures
Authors: Viksna, J
Gilbert, D
Torrance, G
Keywords: protein topology, graph-based representation of structures, structure comparison
Issue Date: 2004
Publisher: Universal Academy Press
Citation: Proceedings of the 15th International Conference on Genome Informatics( GIW 2004), Yokohoma, 14-17 December 2004, 15 (2) 72-81.
Abstract: 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/.
URI: http://bura.brunel.ac.uk/handle/2438/3024
ISSN: 0919-9454
Appears in Collections:Computer Science
Dept of Computer Science Research Papers

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