MolDox takes care of prepping your receptor and ligand(s) from various input formats, defining the docking box dimensions, fast docking, and visualizing the results without the use of external executables.
Inspired by https://github.com/AngelRuizMoreno/Jupyter_Dock
- Easy and fast docking of ligands using Vina Autodock
- Automatic docking box dimensions detection
- Automatic receptor and ligand prepping
- Interactive visualization of docking results
- Simulation of Protein-ligand interactions
MolDox currently supports Python 3.8
- conda | Conda must be installed first
- meeko v0.2 |
pip install meeko==0.2 - Jupyter |
pip install jupyter
It is advised to create separate conda environment
conda create -n moldox python=3.8
conda activate moldox
pip install meeko==0.2
pip install jupyter
MolDox can be simply be installed as:
conda install -c derekvantilborg -c conda-forge -c schrodinger moldox
In special cases, you can install it manually as well.
First clone the git repository:
git clone https://github.com/derekvantilborg/MolDox
Install pymol, openbabel, rdkit, MDAnalysis, pdbfixer, vina, and py3Dmol
conda install -c conda-forge -c schrodinger pymol-bundle
conda install -c conda-forge openbabel
conda install -c conda-forge rdkit
conda install -c conda-forge MDAnalysis
conda install -c conda-forge pdbfixer
conda install -c conda-forge vina
conda install -c conda-forge py3Dmol
The easiest way to get started is opening up the included Jupyter Notebook.
Simply type jupyter-notebook in the terminal and open moldox.ipynb.
An example of this notebook can be found here. It features fetching a pdb + ligand from the internet and re-docking it.
