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.

All systems with the chemical crosslinks tag are shown. [Show all systems]

Show only systems with tag
affinity purification allostery analysis benchmark Brownian dynamics C3 C3b chemical crosslinks chromatin cysteine crosslinks drosophila melanogaster EM EM class average EM density map endogenous complex FoXS FRET glycosylation iC3 in-vivo FRET mass spectrometry model MODELLER multi-state MultiFit native mass spec PMI quantitative crosslinking SAXS TADs X-ray yeast two-hybrid
thumbnail

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): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

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): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Model of Ecm29-proteasome complex PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

eIF3 Modeling PubMed logo

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Exosome modeling PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Mediator Complex PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Nuclear Pore Complex PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Nup133 PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Nup82 Complex PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Nup84 Complex PubMed logo PDB-Dev

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

PDE6 PubMed logo

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

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

Pol II (G) complex PubMed logo PDB-Dev

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1 [more...]

Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

SEA Complex PubMed logo

Modeling of the SEA complex [more...]

Last worked with IMP stable release (master branch): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

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): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08
thumbnail

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): 2.9.0
Last worked with IMP nightly build (develop branch): 2018-12-08