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Integrin

Example of using IMP and PMI to model integrin

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP 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 numpy

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp python/numpy
Tags cysteine crosslinks PMI

This demonstrates the use of IMP and PMI in the modeling of a human integrin. The integrin is modeled partly with low-resolution beads, and partly as idealized helices. We attempt to reconstruct the native structure (PDB entry 2k9j) using cysteine cross-link data [1].

Running

To run, simply run the integrin_modeling.py Python script.

On successful completion, output files (the top-scoring models in PDB format, a trajectory in RMF format, and statistics files) will be found in the output directory. See the IMP tutorial for a full description of these outputs.

Info

[1] Zhu J, Luo BH, Barth P, Schonbrun J, Baker D, Springer TA. Mol Cell. 2009 Apr 24;34(2):234-49. doi: 10.1016/j.molcel.2009.02.022

Author(s): Riccardo Pellarin

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

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