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.
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...]
Human complement modeling [more...]
Benchmark of the AllosMod method [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...]
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...]
Benchmark of the FRET<sub>R</sub> Bayesian restraint [more...]
Example of using IMP and PMI to model glycophorin [more...]
Modeling of the bacterial molecular chaperone GroEL using 3D EM data and cnmultifit [more...]
Integrative model of the γTuSC-Spc110 complex [more...]
Example of using IMP and PMI to model integrin [more...]
Modeling of the yeast Mediator complex [more...]
Benchmark for the sampling procedure used in the Mass Spec paper [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...]
Brownian Dynamics simulations of yeast NPC FG repeats
PDB-Dev
Brownian Dynamics simulations of yeast NPC FG repeats [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...]
Multi-state modeling of the PhoQ two-component system [more...]
Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1 [more...]
Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex [more...]
Benchmark of the SAXS Merge method [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 yeast spindle pole body (SPB) [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...]
Benchmark of the MultiFoXS method [more...]
Comprehensive structure and functional adaptations of the yeast nuclear pore complex
PDB-Dev
Integrative structure determination of the yeast NPC [more...]
Genetic interaction mapping informs integrative structure determination of protein complexes
Integrative Structure Determination using data from point mutant epistatic miniarray profile [more...]
Postmitotic nuclear pore complex assembly pathway
Code for spatiotemporal modeling of the NPC Assembly Pathway [more...]
Sampling exhaustiveness benchmark
Benchmark for sampling exhaustiveness method [more...]
