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Bioinformatics Advance Access originally published online on October 12, 2006
Bioinformatics 2007 23(4):421-426; doi:10.1093/bioinformatics/btl524
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Inherent limitations in protein–protein docking procedures

Noga Kowalsman 1 and Miriam Eisenstein 2,*

1 Department of Biological Chemistry, Weizmann Institute of Science Rehovot, Israel
2 Department of Chemical Research Support, Weizmann Institute of Science Rehovot, Israel

*To whom correspondence should be addressed.


  Abstract

Motivation: The limited success rate of protein–protein docking procedures is generally attributed to structure differences between the bound and unbound states of the molecules. Herein we analyze a large dataset of protein–protein docking results and identify additional parameters that affect the performance of docking procedures.

Results: We find that the distinction between nearly correct models (NCMs) and decoys depends on the size of the interface to be predicted thus setting a limit to the prediction ability of docking procedures, particularly those in which the geometric complementarity descriptor is dominant. The geometric complementarity score in grid-based docking carries a large statistical error which further reduces the distinction between NCMs and decoys. We propose a method for correcting the statistical error and show that the distinction is improved when the docking models are ranked by statistically equivalent scores.

Availability: MolFit can be downloaded from our website http://www.weizmann.ac.il/Chemical_Research_Support/molfit

Contact: miriam.eisenstein@weizmann.ac.il

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on August 9, 2006; revised on October 1, 2006; accepted on October 6, 2006

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