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)   

Raccoon v1.0b for Windows (58 Kbytes)     

Raccoon v1.0 User Manual  (436 Kbytes)

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:

Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905-919.

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.