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.

Create a new conda environment for AMDock and install the required dependencies:

conda create --name AMDock -c conda-forge -c bioconda python=3.9.\* pymol-open-source openbabel pdb2pqr
conda activate AMDock
pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 PyQt5

If you want to install AMDock directly from this repo run:

pip install git+https://github.com/Melarok/AMDock.git

If you want to make changes to AMDock first clone this repo:

git clone https://github.com/Melarok/AMDock.git

After you've made your changes, run the following command from inside the repo to install AMDock:

pip install -e .

Before using AMDock, you most install the PyMOL plugin (grid_amdock.py). If it is not installed automatically follow the instructions:

• Download the grid_amdock.py file from this repo
• 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

Manual, tutorials and test files are located in the Doc folder. They may be out of date. Please check the wiki https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki

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

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