IMP::integrative_docking Namespace Reference

Detailed Description

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: 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. 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 installed data. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Function Documentation

std::string IMP::integrative_docking::get_data_path

(

std::string

file_name

)

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

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

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

std::string IMP::integrative_docking::get_example_path

(

std::string

file_name

)

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

 IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",
model));

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