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