EMageFit

EMageFit is an application to build models of macromolecular assemblies using restraints from EM images (class-averages).

Apart from EM images, the method relies on other types of restraints:

Maximum distance restraints imposing a maximum distance between a pair of residues, as derived from cross-linking experiments. You can of course impose maximum distance between any part of the complex. As shown in the paper, this type of restraint is required to accurately determine the orientation between the subunits of an assembly.
Proximity restraints forcing a pair of subunits to be within a certain distance, suitable for proteomics data.
Excluded volume restraints preventing the components of the assembly from interpenetrating.
Geometric complementarity restraints favoring large contact surfaces between interacting subunits. These restraints can be somewhat useful if the subunits of the assembly are expected to have large contact surfaces. Among all of the restraints considered here, they are the least useful.

EMageFit samples for good conformations of the macromolecular assembly using multiple molecular docking (optional, but it can be very useful), Simulated Annealing Monte Carlo optimization, and sampling with the discrete optimizer DOMINO. It is also straightforward to incorporate other restraints to the method.

If available, EMageFit will use the docking program HEXDOCK to do docking between subunits that are related by cross-links. But it is worth mentioning that EMageFit can also work with any other docking program, or simply using the cross-linking restraints and no docking at all.

More detail on the functioning of EMageFit can be found on the protocol page, and many of the scripts and utilities are documented on the scripts page.

Examples:

Modeling of 3sfd

Info

Author(s): Javier Velazquez-Muriel

Maintainer: benmwebb

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:

Javier A. Velazquez-Muriel, Keren Lasker, Daniel Russel, Jeremy Phillips, Benjamin M. Webb, Dina Scheidmann, Andrej Sali, “Assembly of macromolecular complexes by satisfaciton of spatial restraints from electron microscopy images”, Proc Natl Acad Sci USA 109(46), 18821-18826, 2012.