Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics 2004, GCB 2004, October 4-6, 2004, Bielefeld, Germany P-53, 65-74 (2004).

GI, Gesellschaft für Informatik, Bonn


Robert Giegerich (ed.), Jens Stoye (ed.)

Copyright © GI, Gesellschaft für Informatik, Bonn


A method for fast approximate searching of polypeptide structures in the PDB

Hanjo Täubig , Arno Buchner and Jan Griebsch


The main contribution of this paper is a novel approach for fast searching in huge structural databases like the PDB. The data structure is based on an adaption of the generalized suffix tree and relies on an translationand rotation-invariant representation of the protein backbone. The method was evaluated by applying structural queries to the PDB and comparing the results to the established tool SPASM. Our experiments show that the new method reduces the query time by orders of magnitude while producing comparable results.

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GI, Gesellschaft für Informatik, Bonn
ISBN 3-88579-382-2

Last changed 04.10.2013 18:03:54