Personal tools


Hex is a rigid body protein-protein docking program which is ranking solutions based on (soft) shape and electrostatic complementarity. It uses (very) Fast-Fourier-Transformation in spherical coordinates to perform a systematic search through the whole orientation space (sampling millions of orientations).

The home page with license and download links is:

To install the program...

  1. Download generic runtime and configure script:

    cd /tmp
  2. Download the executable matching your system (the static version is most generic but lacks OpenGL support):

  3. Run the installation script:

    chmod +x  hex_configure.bin

    Choose an installation path (e.g. /usr/local/lib/hex) and answer 'y' to all other questions.

    Note: The installation script fails if some old$HEX_ROOT and $HEX_CACHE are set but point to a non-existing folder -- override them with an empty string, for example, 'export HEX_ROOT= ' and 'export HEX_CACHE= '

  4. Adapt environment:

    Add the following variables to your shell login script (example for bash or zsh):

    export HEX_ROOT=/usr/local/lib/hex
    export HEX_CACHE=/home/biskit/hex_cache

    And put hex into the path:

    sudo ln -s /usr/local/lib/hex/bin/hex /usr/local/bin/
  5. Test the Biskit / Hex interface:

    First type 'hex' and make sure you get the fancy user interface of Hex.


    Ubuntu users need to modify run_hex first, see Hex troubleshooting!

    Now test the hex interface (and go for a coffee after typing the command):

    cd biskit/Biskit/Dock

  • see
  • see
  • see
  • see scripts/Dock/
  • see scripts/Dock/
  • see scripts/Dock/
Custom configuration:
see biskit/external/defaults/settings_Mod.cfg (pending conversion to Executor interface)