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Raccoon | AutoDock

by Stefano Forli last modified 2013-02-22 14:44


Raccoon is a graphical interface for preparing AutoDock virtual screenings.


Features

Raccoon automates some of the most common operations performed when preparing a virtual screening:

  • automatic processing of ligand libraries (PDB, MOL2, PDBQT)
  • split multi-structure files (MOL2)
  • generate PDBQT input files
  • multiple receptor conformations
  • flexible residues
  • filter ligands
  • generate configuration files for both AutoGrid and AutoDock.
  • generate scripts for running the virtual screening.


Virtual screenings can be generated for workstations and PBS Linux clusters.

Downloads


Raccoon v1.0b for Linux/Mac (58 Kbytes)    platform_linux.gifplatform_mac_os_x.gif

Raccoon v1.0b for Windows (58 Kbytes)      platform_windows.gif

Raccoon v1.0 User Manual  (436 Kbytes) platform_all_platforms.gif


Installation

Raccoon requires the following software:

  • MGLTools v.1.5.4 or newer installed on your system.
  • although not essential, installing AutoDock is strongly recommended for full access to all the features.


Linux/Mac

  1. Extract all the content of the file raccoon.tar.gz in a directory (i.e. your Desktop)
  2. Open a terminal, cd to the directory where the file “raccoon.py” has been extracted and type:
    pythonsh raccoon.py
  3. If the “pythonsh” command is not recognized by the terminal, specify the full path corresponding to your MGLTools installation, for example:
    Linux
    /usr/local/mgltools_i86Linux2_1.5.4/bin/pythonsh raccoon.py

    Mac
    /Library/MGLTools/1.5.4/bin/pythonsh raccoon.py
  4. (Optional) Add an alias to your .bashrc or .cshrc for running Raccoon:
    Bash
    alias raccoon='/usr/local/mgltools_i86Linux2_1.5.4/bin/pythonsh /full/path/to/raccoon.py'

    C-shell
    alias raccoon '/usr/local/mgltools_i86Linux2_1.5.4/bin/pythonsh /full/path/to/raccoon.py'

Windows

  1. Extract all the files contained in the file raccoon_win.zip in the MGL Tools installation directory (default: “C:\Program Files\MGLTools 1.5.4”)
  2. Edit the file raccoon.bat, if necessary, to match your installation path:
    set MGLPYTHONPATH=C:\Program Files\MGLTools 1.5.4"
    C:\Python25\python.exe" "%MGLPYTHONPATH%\raccoon.py"
  3. (Optional) Create a link to raccoon.bat on your desktop by dragging the icon of the file to  the Desktop while pressing the Alt-key.



Citation and reference

If you use Raccoon for your dockings, please cite the software as following:

Stefano Forli, "Raccoon|AutoDock VS: an automated tool for preparing AutoDock virtual screenings", http://autodock.scripps.edu/resources/raccoon (accessed xx/xx/2010)


Help and support

As for all the MGL software, community and developers support for Raccoon is available through the Internet.
Any suggestions for improvements or bug reports are welcome.

  • Mailing list

Subscribe to the AutoDock mailing list as described here: http://autodock.scripps.edu/mailing_list

The best way to report a problem is to write a message with the prefix "Raccoon: " in the subject and a short description of the issue.
Any error messages and further details should be reported in the body of the email.

  • Forum

Register to the MGL Forum: http://mgl.scripps.edu/forum/
Search for threads related to the issue encountered, and if open a new thread if necessary.


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