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pyMLP: Molecular Lipophilicity Potential evaluator

Presentation

pyMLP is a program computing the molecular lipophilicity potential map of proteins.

pyMLP takes a protein .pdb file as input and output a .dx map file easily visualized in many molecular visualization packages such as VMD, Pymol, Chimera, ...

References

Please include this reference in published work using pyMLP:

  • Broto P., Moreau G., Vandycke C. - Molecular structures: Perception, autocorrelation descriptor and sar studies. System of atomic contributions for the calculation of the n-octanol/water partition coefficients, Eu. J. Med. Chem. 1984, 19.1, 71-78

  • Laguerre M., Saux M., Dubost J.P., Carpy A. - MLPP: A program for the calculation of molecular lipophilicity potential in proteins, Pharm. Sci. 1997, 3.5-6, 217-222

This program was developed in python as a platform independent equivalent of MLPP (see references). As a result pyMLP may run on any platform supported by Python and Numpy.

INSTALLATION

In order to launch pyMLP you will need:

  • a working python installation (http://www.python.org) (tested with version 2.4 and 2.5) (any desktop oriented Linux distribution should have already one installed)
  • a working numpy installation (http://numpy.scipy.org/) (any scientific friendly Linux distribution should have it in its repository)

(pyMLP was reported to work on win32 with Enthought's Python Sumo-Distribution for Windows (http://www.enthought.com/))

With a properly configured python + numpy install, you just have to input this command to the CLI (command line interface):

python pyMLP.py

Optional

In order to have pyMLP.py available from any directory you can copy it in your PATH (after enabling direct execution):

chmod +x pyMLP.py
cp pyMLP.py /usr/local/bin/

Then you can directly launch pyMLP that way:

pyMLP.py

USAGE

pyMLP takes a .pdb file as input and output a .dx map file easily visualized in many molecular visualization packages such as VMD, Pymol, Chimera, ...

Please run pyMLP.py --help for detailed instructions.

Simple examples:

  • Command to calculate foo.dx the lipophilicity potential map of foo.pdb: (assuming pyMLP.py is in your PATH and foo.pdb in the current directory this command will create foo.dx in the current directory)
pyMLP.py -i foo.pdb
  • Command that will achieve exactly the same thing as the one above but be more verbose about what is being done:
pyMLP.py -v -i foo.pdb

FOOTNOTE

Feel free to criticize pyMLP code: it needs some serious refactoring and way more comments ... alas it works for me ... sorry

(from the quick-n-dirty-dev-dpt)

last modified March 28, 2007 by Julien Lefeuvre