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 permanently archived (via DOIs) at Zenodo; newer systems are also deposited at PDB-Dev.

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.

All systems with the X-ray tag are shown. [Show all systems]

40S•eIF1•eIF3 Complex

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

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks MODELLER PMI1 X-ray

Integrative structures of the human Cop9 signalosome PDB-Dev

Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks MODELLER PMI X-ray

Model of Ecm29-proteasome complex PDB-Dev

Regulation of 26S proteasome via interaction with Ecm29 [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks PMI X-ray

Exosome modeling PDB-Dev

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

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks endogenous complex PMI1 X-ray

γTuSC-Spc110 Complex PDB-Dev

Integrative model of the γTuSC-Spc110 complex [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks cryo-EM X-ray

Mediator Complex PDB-Dev

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

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks EM density map PMI1 X-ray

Integrative structures of the Nef-CD4-AP2 complex PDB-Dev

Integrative structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks MODELLER PMI X-ray

Nuclear Pore Complex PDB-Dev

Modeling of the yeast Nuclear Pore Complex [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags affinity purification chemical crosslinks EM class average EM density map FoXS PMI1 X-ray

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

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks EM class average FoXS MODELLER multi-state SAXS X-ray

NuRD subcomplexes

Integrative modeling of NuRD sub-complexes [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks COSMIC cryo-EM NMR PMI SEC-MALLS X-ray

Modeling of Pom152 PDB-Dev

Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags EM class average EM density map FoXS MODELLER PMI1 SAXS X-ray

Smc5/6-Nse2/5/6 complex PDB-Dev

Integrative modeling of the Smc5/6-Nse2/5/6 complex using comparative modeling and chemical crosslinks. [more...]

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks coiled-coils cryo-EM ISAMBARD PMI X-ray

PMI RNAPII Modeling Tutorial

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

Last worked with IMP stable release (main branch): 2.21.0

Last worked with IMP nightly build (develop branch): 2024-06-02

Tags chemical crosslinks EM density map PMI X-ray

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

Integrative structures of the A3G-CRL5-Vif-CBFb complex PDB-Dev

Integrative structure determination of the A3G-CRL5-Vif-CBFβ complex [more...]

Tags chemical crosslinks MODELLER PMI X-ray

Genetic interaction mapping informs integrative structure determination of protein complexes

Integrative Structure Determination using data from point mutant epistatic miniarray profile [more...]

Tags MODELLER pEMAP PMI X-ray