IMP::integrative_docking Namespace Reference

Pairwise docking incorporating additional data. More...

Detailed Description

Pairwise docking incorporating additional data.

idock

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 for pairwise protein docking, followed by filtering based on fit to the experimental data, clustering and composite scoring.

Examples:

• Docking of PCSK9

Info

Author(s): Dina Schneidman

Maintainer: duhovka

License: GPL 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

Standard module functions
All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to one of this module's data files. More...
std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...

Function Documentation

std::string IMP::integrative_docking::get_data_path

(

std::string

file_name

)

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

std::ifstream in(IMP::integrative_docking::get_data_path("data_library"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note

Each module has its own data directory, so be sure to use this function from the correct module.

std::string IMP::integrative_docking::get_example_path

(

std::string

file_name

)

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::integrative_docking::get_example_path("example_protein.pdb"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note

Each module has its own example directory, so be sure to use this function from the correct module.