AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input files, define the search space (box) and perform docking under user’s supervision.

Version 1.6.x for Linux (Build 1.6.1-beta)

DOCUMENTATION

Manual, tutorials and test files are located in Doc folder. (May be out of date. Please check the wiki)

Cite us

Valdes-Tresanco, M.S., Valdes-Tresanco, M.E., Valiente, P.A. and Moreno E. AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biol Direct 15, 12 (2020). https://doi.org/10.1186/s13062-020-00267-2

INSTALL

Installation can be carried out in two ways

1. (For Linux only) Using a conda environment.

Note: macOS users can use this procedure, however, PyMOL must be compiled using this environment's Python interpreter, since there is no working version of PyMOL for mac in the anaconda repositories.

To do this, proceed as follows:

If you don't have conda installed, please visit the Miniconda download page.

Those with an existing conda installation may wish to create a new conda "environment" to avoid conflicts with what you already have installed. To do this:

conda create --name AMDock python=3.9
conda activate AMDock

(Note that you would need to perform the "conda activate" step every time you wish to use AMDock in a new terminal; it might be appropriate to add this to your start-up script. Creating a new environment should not be necessary if you only use conda for AMDock.)

Once this is done, type:

conda install -c conda-forge pymol-open-source openbabel pdb2pqr

and finally:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 PyQt5
python -m pip install AMDock

2. Using the OS Python 3 environment. To do this, proceed as follows:

   sudo apt install pymol openbabel

(Note that this version of AMDock works with openbabel 3.x)

python3 -m pip install pdb2pqr PyQt5
python3 -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
python3 -m pip install AMDock

Before using AMDock, you most install the PyMOL plugin (grid_amdock.py).

If it does not appear please follow the instructions:

• Download the grid_amdock.py file
• Open PyMOL > Plugins > Manager Plugins > Install New Plugin > Choose File and select the grid_amdock.py file
• Restart PyMOL

To open AMDock, type in the terminal:

AMDock

Note: You can add this line to the .bashrc file to activate de AMDock conda environment and execute AMDock directly

alias amdock="conda activate AMDock; AMDock"

For macOS users,

To view the update history, please check Changes_History file

TUTORIALS

Please, check the wiki https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki

This project is possible thanks to the Open Source license of the JetBrains programs.