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NPC transport simulations

Simulating nucleocytoplasmic transport using IMP

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crossWarning: these files have not yet been verified to work with the latest version of IMP. We will update this page when they have been. The files are also available at GitHub.
Additional software needed to use these files: IMP scikit-learn matplotlib 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

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

module load Sali
module load imp python3/scikit python3/matplotlib
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.