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Bioinformatics Advance Access published online on September 23, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn497
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DOCKGROUND Protein-Protein Docking Decoy Set

Shiyong Liu 1, Ying Gao 1 and Ilya A. Vakser 1,2,*

1Center for Bioinformatics and 2Department of Molecular Biosciences, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.

*To whom correspondence should be addressed. Prof. Ilya A. Vakser, E-mail: vakser{at}ku.edu


  Abstract

Summary: A protein-protein docking decoy set is built for the DOCKGROUND unbound benchmark set. The GRAMM-X docking scan was used to generate 100 non-native and at least one near-native match per complex for 61 complexes. The set is a publicly available resource for the development of scoring functions and knowledge-based potentials for protein docking methodologies.

Availability: The decoys are freely available for download at http://dockground.bioinformatics.ku.edu/UNBOUND.

Contact: vakser{at}ku.edu

Associate Editor: Prof. Burkhard Rost

Received on April 9, 2008; revised on September 12, 2008; accepted on September 16, 2008

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