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Nucleic Acids Research 2006 34(Web Server issue):W20-W23; doi:10.1093/nar/gkl273
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

PAST: fast structure-based searching in the PDB

Hanjo Täubig, Arno Buchner* and Jan Griebsch*

1 Efficient Algorithms Group, Department of Computer Science, Technische Universität München Boltzmannstrasse. 3, 85748 Garching, Germany

*To whom correspondence should be addressed. Email: teaubig{at}in.tum.de

*Correspondence may also be addressed to Arno Buchner. Email: buchner{at}in.tume.de

Received February 14, 2006. Revised March 19, 2006. Accepted April 3, 2006.

PAST is a new web service providing fast structural queries of the Protein Data Bank. The search engine is based on an adaptation of the generalized suffix tree and relies on a translation- and rotation-invariant representation of the protein backbone. The search procedure is completely independent of the amino acid sequence of the polypeptide chains. The web service works best with, but is not necessarily limited to, shorter fragments such as functional motifs—a task that most other tools do not perform well. Usual query times are in the order of seconds, allowing a truly interactive use. Unlike most established tools, PAST does not prefilter the dataset or exclude parts of the search space based on statistical reasoning. The server is freely available at http://past.in.tum.de/.


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