\brief Pairwise docking incorporating additional data.

# idock {#idock_bin}

Pairwise docking incorporating additional data.

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

Additionally the protocol calculates SOAP score based on an atomic statistical potential.
 - a SOAP score (SOAP)

The protocol proceeds by first sampling complex models using
[PatchDock](http://bioinfo3d.cs.tau.ac.il/PatchDock/) for pairwise protein
docking, followed by
\ref idock_progs "filtering based on fit to the experimental data",
clustering and composite scoring.

_Examples_:
 - [Docking of PCSK9](@ref idock_pcsk9)

# Info

_Author(s)_: Dina Schneidman

_Maintainer_: `duhovka`

_License_: [GPL](https://www.gnu.org/licenses/gpl.html)
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU 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. 2011 Mar;173(3):461-71.
 - Schneidman-Duhovny et al. A method for integrative structure determination of protein-protein complexes. Bioinformatics. 2012;28(24):3282-9.
 - Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. Optimized atomic statistical potentials: Assessment of protein interfaces and loops. Bioinformatics. 2013;29(24):3158-66
