SMTDock

SMTDock is a novel approach to the protein-ligand docking problem based on AMDock, which employs an SMT-solver to predict the binding pose of a ligand.

Setup

A makefile is provided to setup the system through the following commands:

1. Initial environment setup:

   make setup     # create the virtual environment and install dependencies

2. Activate the python environment:

   . .venv/bin/activate

Usage

SMTDock can be run using the command:

python3 main.py protein ligand

where a related folder must already exist.

To add a new protein/ligand pair, follow the execution of AMDock using the information provided in the official tutorial.

Example

As an example, to find the binding pose of the ligand Adenosine with the protein A2A, run the command:

python3 main.py a2a adn

The output of the program, including information on the new pose (in pdb format) and the related energy and runtime, can be found in the subfolder smtdock.

Machine environment

The program has been tested on an Apple device; for different architectures, the setup steps may include some differences.