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Integrin

Example of using IMP and PMI to model integrin

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tickVerified to work with the latest stable IMP release (2.20.2). 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 Wynton cluster to run this system, run:

module load Sali
module load imp python3/numpy
Tags cysteine crosslinks PMI1

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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