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 cryo-EM tag are shown. [Show all systems]

Show only systems with tag
affinity purification allostery analysis benchmark Brownian dynamics C3 C3b chemical crosslinks chromatin coiled-coils COSMIC cryo-EM cryo-ET cysteine crosslinks drosophila melanogaster EM EM class average EM density map endogenous complex escape mutations FCS FoXS FRET glycosylation iC3 in-vivo FRET ISAMBARD mass spectrometry model MODELLER multi-state MultiFit nanobodies native mass spec NMR pEMAP PMI PMI1 quantitative crosslinking SAXS SEC-MALLS shape-complementarity spatiotemporal TADs threading X-ray yeast two-hybrid
thumbnail

γTuSC-Spc110 Complex PubMed logo 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
thumbnail

Nanobody epitopes on SARS-CoV-2 spike protein PubMed logo

Integrative modeling of nanobody binding modes to the SARS-CoV-2 Spike protein [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 escape mutations nanobodies PMI shape-complementarity
thumbnail

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
thumbnail

Smc5/6-Nse2/5/6 complex PubMed logo 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

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

thumbnail

Comprehensive structure and functional adaptations of the yeast nuclear pore complex PubMed logo PDB-Dev

Integrative structure determination of the yeast NPC [more...]

Tags chemical crosslinks cryo-EM PMI