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Inherent limitations in protein-protein docking procedures.
- Source :
-
Bioinformatics (Oxford, England) [Bioinformatics] 2007 Feb 15; Vol. 23 (4), pp. 421-6. Date of Electronic Publication: 2006 Oct 12. - Publication Year :
- 2007
-
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.<br />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.<br />Availability: MolFit can be downloaded from our website http://www.weizmann.ac.il/Chemical&#95;Research&#95;Support/molfit.<br />Supplementary Information: Supplementary data are available at Bioinformatics online.
Details
- Language :
- English
- ISSN :
- 1367-4811
- Volume :
- 23
- Issue :
- 4
- Database :
- MEDLINE
- Journal :
- Bioinformatics (Oxford, England)
- Publication Type :
- Academic Journal
- Accession number :
- 17040920
- Full Text :
- https://doi.org/10.1093/bioinformatics/btl524