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Bioinformatics Advance Access originally published online on September 25, 2008
Bioinformatics 2008 24(23):2780-2781; doi:10.1093/bioinformatics/btn507
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Searching protein structure databases with DaliLite v.3

L. Holm 1,2,*, S. Kääriäinen 2, P. Rosenström 2 and A. Schenkel 2

1Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland

*To whom correspondence should be addressed.


  Abstract

The Red Queen said, ‘It takes all the running you can do, to keep in the same place.’ Lewis Carrol

Motivation: Newly solved protein structures are routinely scanned against structures already in the Protein Data Bank (PDB) using Internet servers. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The number of known structures continues to grow exponentially. Sensitive—thorough but slow—search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the PDB than seconds in a day. The brute-force solution would be to distribute the individual comparisons on a massively parallel computer. A frugal solution, as implemented in the Dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. This note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a PC.

Availability: The Dali server for protein structure database searching at http://ekhidna.biocenter.helsinki.fi/dali_server is running DaliLite v.3. The software can be downloaded for academic use from http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3.

Contact: liisa.holm{at}helsinki.fi

Associate Editor: Thomas Lengauer

Received on June 10, 2008; revised on August 14, 2008; accepted on September 22, 2008

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