Installation and Setup

This guide provides step-by-step instructions for installing the GDEE platform and all required dependencies.

System Requirements

Operating System: - Linux (Ubuntu 18.04+, or equivalent)

Python Environment: - Python 3.7 or higher - pip package manager - Virtual environment support (recommended)

Python Package Requirements - numpy>=1.14 - mdanalysis>=0.20 - mpi4py>=3.0 - path>=13.0 - biopython>=1.75 - oddt>=0.7 - openbabel-wheel>=3.1.1.1 - six >= 1.17.0 - scipy == 1.9.0

Core Installation

  1. Create Python Virtual Environment

# Create and activate virtual environment
python3 -m venv gdee-env
source gdee-env/bin/activate

  1. Install six and scipy

    Note

    scipy==1.9.0 is required for compatibility with the oddt package

pip install six>=1.17.0 scipy==1.9.0

  1. Install GDEE Platform

# install from source
git clone https://github.com/protein-modelling-itqb/gdee.git
cd gdee/package
pip install -e .

Required External Programs

The GDEE platform requires several external programs. Please follow the official installation documentation for each tool to ensure you have the most up-to-date installation procedures.

MODELLER Installation

MODELLER is required for 3D structure modeling of protein variants.

Installation: Please follow the official MODELLER installation guide at https://salilab.org/modeller/download_installation.html

Requirements: - Academic license registration required - Python bindings must be installed in your GDEE virtual environment

MGLTools Installation

MGLTools is required for converting PDB files to PDBQT format for docking.

Installation: Please follow the official MGLTools installation guide at https://ccsb.scripps.edu/mgltools/downloads/

Configuration in GDEE:

# In your GDEE script, specify the MGLTools installation path
eng.programs["mgltools"] = "/path/to/mgltools_installation"

AutoDock Vina Installation

AutoDock Vina is required for molecular docking calculations.

Installation: Please follow the official AutoDock Vina installation guide at https://github.com/ccsb-scripps/AutoDock-Vina

Configuration in GDEE:

# In your GDEE script, specify the Vina executable path
eng.programs["vina"] = "/path/to/vina"

Vinardo Installation (Optional)

Vinardo is available as a scoring function in the Smina program.

Installation: Please follow the official Smina installation guide at https://sourceforge.net/projects/smina/

Configuration in GDEE:

# In your GDEE script, specify the Smina executable path
eng.programs["vinardo"] = "/path/to/smina"

VoroMQA Installation (Optional)

VoroMQA is used for model quality assessment using Voronoi tessellation.

Installation: Please follow the official Voronota installation guide at https://github.com/kliment-olechnovic/voronota

Configuration in GDEE:

# In your GDEE script, specify the VoroMQA executable path
eng.programs["voromqa"] = "/path/to/voronota-voromqa"

Next Steps

After successful installation:

  1. Review the Usage Instructions for workflow examples

  2. Ensure all external programs are properly configured in your GDEE scripts

  3. Test your installation with a simple workflow to verify all dependencies work correctly