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 chemical crosslinks tag are shown. [Show all systems]
Modeling the structures of complexes between the 26S proteasome and proteasome interacting proteins [more...]
Determination of the molecular architecture of the 40S•eIF1•eIF3 translation initiation complex [more...]
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...]
Integrative threading of protein structure using secondary structure elements [more...]
Model of Ecm29-proteasome complex
PDB-Dev
Regulation of 26S proteasome via interaction with Ecm29 [more...]
Data and scripts to model eIF3 from mass spec data [more...]
Integrative Modeling of Yeast Exocyst Complex [more...]
Modeling exosome complexes from cross-link MS data [more...]
Integrative model of the γTuSC-Spc110 complex [more...]
Modeling of the yeast Mediator complex [more...]
Nanobody epitopes on SARS-CoV-2 spike protein
Integrative modeling of nanobody binding modes to the SARS-CoV-2 Spike protein [more...]
Integrative structures of the Nef-CD4-AP2 complex
PDB-Dev
Integrative structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex [more...]
Modeling of the yeast Nuclear Pore Complex [more...]
Modeling of the Nup133 subunit of the Nuclear Pore Complex [more...]
Modeling of the Nup82 subcomplex of the Nuclear Pore Complex [more...]
Modeling of the Nup84 subcomplex of the Nuclear Pore Complex [more...]
Integrative modeling of NuRD sub-complexes [more...]
Modeling of the phosphodiesterase (PDE6) [more...]
Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1 [more...]
Modeling of the SEA complex [more...]
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...]
Modeling of the TFIIH complex using chemical cross-links and electron microscopy (EM) density maps [more...]
Tutorial that demonstrates the modeling of RNA Polymerase II using Electron Microscopy density and chemical crosslinks [more...]
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...]
Comprehensive structure and functional adaptations of the yeast nuclear pore complex
PDB-Dev
Integrative structure determination of the yeast NPC [more...]
