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Nuclear Pore Complex

Modeling of the yeast Nuclear Pore Complex PubMed logo PDB-Dev

tickVerified to work with the latest stable IMP release (2.18.0). The files are also available at GitHub.
Additional software needed to use these files: IMP MODELLER numpy install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp modeller numpy

UCSF logo To set up the environment on the UCSF Wynton cluster to run this system, run:

module load Sali
module load imp modeller python3/numpy
Tags affinity purification chemical crosslinks EM class average EM density map FoXS PMI1 X-ray


These scripts demonstrate the use of IMP in the modeling of the yeast NPC complex using diverse types of data as described in Seung Joong Kim, et al.'s 2018 NPC article published in Nature.

The scripts work with the IMP (version 2.6). A default build of IMP compiled with the IMP::npc module should work, but for most effective sampling, it should be built with MPI so that replica exchange can be used.

List of files and directories:

Compiling IMP with NPC-specific module:

Running the IMP scripts for the NPC complex:

  1. Inner-ring components (Nup157, Nup170, Nup188, Nup192, Nic96, Nup53, Nup59, Ndc1, Pom34, and Pom152 NTD)
  1. Outer-ring components (Nup82 and Nup84 complexes)



Author(s): Seung Joong Kim

License: CC-BY-SA-4.0. This work is freely available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License.

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