Summary

This page shows a number of applications of IMP to biological systems. They can be adapted to tackle other similar problems, or to add new input data to an existing system.

Each system links to its web page, where all the input files can be found, complete with running instructions. Most systems are also permanently archived (via DOIs) at Zenodo.

Every system is periodically tested with the latest version of IMP to make sure it works. The most recent version of IMP that it works with is shown below (or see all builds).

See the IMP manual for information on adding a new system to this page.

Show only systems with tag
affinity purification allostery benchmark C3 C3b chemical crosslinks chromatin cysteine crosslinks drosophila melanogaster EM class average EM density map endogenous complex FoXS FRET glycosylation iC3 mass spectrometry model MODELLER multi-state MultiFit native mass spec PMI quantitative crosslinking SAXS TADs X-ray
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26S-PIPs complex PubMed logo

Modeling the structures of complexes between the 26S proteasome and proteasome interacting proteins [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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40S•eIF1•eIF3 Complex PubMed logo

Determination of the molecular architecture of the 40S•eIF1•eIF3 translation initiation complex [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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AllosMod benchmark PubMed logo

Benchmark of the AllosMod method [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Human Complement PubMed logo

Human complement modeling [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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eIF3 Modeling PubMed logo

Data and scripts to model eIF3 from mass spec data [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Exosome modeling PubMed logo

Modeling exosome complexes from cross-link MS data [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Modelling of a region of the fly genome

Example of using IMP to model a region of the Fly genome https://integrativemodeling.org/systems/ [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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FRET Benchmark PubMed logo

Benchmark of the FRETR Bayesian restraint [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Glycophorin

Example of using IMP and PMI to model glycophorin [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Integrin

Example of using IMP and PMI to model integrin [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Mediator Complex PubMed logo

Modeling of the yeast Mediator complex [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Mass Spec Benchmark PubMed logo

Benchmark for the sampling procedure used in the Mass Spec paper [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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Nup84 Complex PubMed logo

Modeling of the Nup84 subcomplex of the Nuclear Pore Complex [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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PDE6 PubMed logo

Modeling of the phosphodiesterase (PDE6) [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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PhoQ PubMed logo

Multi-state modeling of the PhoQ two-component system [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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SAXS Merge benchmark PubMed logo

Benchmark of the SAXS Merge method [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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TFIIH complex PubMed logo

Modeling of the TFIIH complex using chemical cross-links and electron microscopy (EM) density maps [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07
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IMP Tutorial

Tutorial that demonstrates the modeling of RNA Polymerase II using Electron Microscopy density and chemical crosslinks [more...]

Last worked with IMP stable release (master branch): 2.7.0
Last worked with IMP nightly build (develop branch): 2017-04-07

warning The following systems are still under development and have not yet been tested against the public release of IMP:

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MultiFoXS benchmark

Benchmark of the MultiFoXS method [more...]

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Nup133 PubMed logo

Modeling of the Nup133 subunit of the Nuclear Pore Complex [more...]

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Nup82 Complex PubMed logo

Modeling of the Nup82 subcomplex of the Nuclear Pore Complex [more...]

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SEA Complex PubMed logo

Modeling of the SEA complex [more...]