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NPC transport simulations

Simulating nucleocytoplasmic transport using IMP

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warningThese files work only with a nightly build of IMP on or after 2026-01-20, not the stable release. The files are also available at GitHub.
Additional software needed to use these files: IMP scikit-learn matplotlib protobuf 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 scikit-learn matplotlib protobuf

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

module load Sali
module load imp python2/scikit python2/matplotlib python2/protobuf
Tags Brownian dynamics Coarse-grained modeling NPC Nuclear pore complex transport

NPC Simulations Utility Files and Datasets

User's Manual

A detailed User's Manual in PDF format is available in this folder.

scripts/

Utility scripts used for initiating and analyzing the simulation. See tutorial for details on how and when to use key scripts.

tutorials/

Tutorial in Jupyter Notebook format for running a basic simulation in a simplified setting + basic analysis

test/

Test script for running a basic simulation in a simplified setting + basic analysis

data/cryoET/

In situ cryo-electron tomography (cryoET) map of the NPC's central channel used for validation of simulated NPC morphology

models/NPC2018/

Kim et al. 2018 model of the NPC scaffold used in this work (see also User's manual)

Reference

Raveh B*, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP*, Cowburn D*, Sali A*. Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport. Proc Nat Acad Sci (2025), in press.

License

See LICENSE file.