This is a protocol for pairwise protein docking, in which additional experimental information about the protein-protein complex is incorporated into the docking procedure to greatly improve the accuracy of predictions. This method succeeds in producing a near-native model among the top 10 models in 42–82% of cases, while state-of-the-art docking methods succeed only in 30–40% of cases, depending on the benchmark and accuracy criterion.

The protocol can currently incorporate data from the following sources:

the pair-distance distribution function of the complex from a SAXS profile
2D class average images of the complex from negative-stain EM micrographs (EM2D)
a 3D density map of the complex from single-particle negative-stain EM micrographs (EM3D)
residue type content at the protein interface from NMR spectroscopy (NMR-RTC)
chemical cross-linking detected by mass spectrometry (CXMS).

The protocol proceeds by first sampling complex models using PatchDock for pairwise protein docking, followed by filtering based on fit to the experimental data, conformational refinement using FiberDock and composite scoring. Third, good-scoring representatives of clusters of models are picked as final models.

Examples:

Docking of PCSK9

Info

Author(s): Dina Schneidman

Maintainer: duhovka

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 2010
Schneidman-Duhovny et al. A method for integrative structure determination of protein-protein complexes: application to a therapeutical antibody-antigen complex. submitted