Inherent limitations in protein-protein docking procedures.
BACKGROUND
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.


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Kowalsman
Noga
N
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
Eisenstein
Miriam
M
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins