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lambada-align

Automatic membrane protein orientation and alignment

LAMBADA automates the adjustment of 3D membrane protein structures with lipid bilayers.

:: FEATURES ::

  • Automatic orientation of the protein according to its hydrophobic surface profile
  • Automatic alignment of the membrane
  • Output of the combined membrane protein system ready for protein embedding

:: NEWS ::

2012-09-28 The first release of LAMBADA is available for download.

:: INSTALLATION & QUICK START ::

  1. Download the LAMBADA archive from the project download website.
  2. Unpack the LAMBADA archive

    tar -xvzf lambada.tar.gz (LAMBADA should work already now by typing perl lambada/lambada.)

  3. Copy the folder to your lib directory

    cp -r lambada/ ~/lib/

  4. Make LAMBADA executable (e.g. chmod 755 ~/lib/lambada/lambada)

    chmod 755 ~/lib/lambada/lambada

  5. Set a soft link to the LAMBADA executable in your bin directory

    ln -s ~/lib/lambada/lambada ~/bin/lambada

Run LAMBADA by typing:

lambada -f1 protein.gro -f2 membrane.gro

Get the program help by typing:

lambada -h

:: DOCUMENTATION ::

We provide installation instructions and a manual on this program's project page.

Example applications of LAMBADA in combination with the protein embedding procedure can be found on the project page of InflateGRO2.

:: REFERENCES ::

If you use LAMBADA for publication, please cite Schmidt, T. H. & Kandt, C. LAMBADA & InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations. Biophysical Journal 102, 173a (2012). http://dx.doi.org/10.1016/j.bpj.2011.11.938

Electronic documents should include a direct link to the LAMBADA hosting page: https://github.com/THSchmidt/lambada-align

For geeks we provide a QR Code, referencing to this Google Project page: QR Code 72dpi QR Code 300dpi

:: RELATED PROJECTS ::

After using the LAMBADA protein orientation you can use our new version of the commonly used embedding routine InflateGRO2: https://github.com/THSchmidt/inflategro2

The InflateGRO2 project page includes a full tutorial for the system setup of a set of membrane proteins with representative structural characteristics, using both LAMBADA & InflateGRO2.