IMP: The Integrative Modeling Platform

Daniel Russel, Ben Webb, Keren Lasker and Andrej Sali

IMP Overview

Our broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, such as the ribosome and the nuclear pore complex (NPC). Detailed structural characterization of assemblies is generally impossible by any single existing experimental or computational method. This barrier can be overcome by hybrid approaches that integrate data from diverse biochemical and biophysical experiments (eg, x-ray crystallography, NMR spectroscopy, electron microscopy, immuno-electron microscopy, footprinting, chemical cross-linking, FRET spectroscopy, small angle X-ray scattering, immunoprecipitation, and genetic interactions).

We formulate the hybrid approach to structure determination as an optimization problem, the solution of which requires three main components:

the representation of the assembly,
the scoring function and
the optimization method.

The ensemble of solutions to the optimization problem embodies the most accurate structural characterization given the available information.

We created IMP, the Integrative Modeling Platform, to make it easier to implement such an integrative approach to structural and dynamics problems. IMP is designed to allow mixing and matching of existing modeling components as well as easy addition of new functionality. We encourage and support contributions from other laboratories.

Citing IMP

If you use IMP in work which leads to a publication you should cite the main IMP paper as well as papers for each of the modules that you used. See the list of the module pages to find the publications covering each module.

Current Status

Many parts of IMP are complete and tested. It contains a wide variety of general purpose restraints for restraining the geometry of sets of spheres and points as well to fit models to EM density maps. We have several active developers and contributors who can quickly answer questions about using IMP.

Planned Changes

Add better support for Atoms and PDBs. Currently PDBs can be read and atomic structure manipulated, but there is no support for writing PDBs and no atomic force fields.
Add SAXS-based restraints

Contributions

We are currently looking for people to contribute restraints on any types of experimental data which are not covered already such as NMR data.

Why add contribute to IMP

If you write code using IMP you should consider adding your code as a module in the IMP repository. Add your code as module in IMP

means your code is built and tested every night on a wide variety of platforms
makes it easier for other IMP users to use your code
makes it easier for other IMP users to find your code