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Bioinformatics. 2007 Feb 15;23(4):421-6. Epub 2006 Oct 12.

Inherent limitations in protein-protein docking procedures.

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  • 1Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.

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.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
17040920
DOI:
10.1093/bioinformatics/btl524
[PubMed - indexed for MEDLINE]
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