EasyDock - Python module to automate molecular docking

EasyDock automates the entire docking process from molecule preparation to result analysis, supporting multiple docking programs and providing organized result storage.

Key Features

• Multiple Docking Programs: Support for Vina, Gnina/Smina, QVina, Vina-GPU and their derivatives
• Automated Preparation: Molecule validation, salt removal, and stereoisomer enumeration
• Flexible Protonation: Multiple methods including MolGpKa, Uni-pKa, Chemaxon, and pkasolver
• Distributed Computing: Scale across multiple servers using Dask
• Database Storage: All results organized in SQLite databases
• PLIF Analysis: Protein-ligand interaction fingerprints for detailed analysis
• Resumable Calculations: Interrupted runs can be continued seamlessly

Quick Start

# Create environment
conda env create -f env.yml -n easydock
# or use mamba (should be faster) 
mamba env create -f env.yml -n easydock

# Run docking
easydock -i input.smi -o output.db --program vina --config config.yml --protonation molgpka -c 4 --sdf

Documentation

https://easydock.readthedocs.io/en/latest/

Licence

BSD-3

Citation

Minibaeva, G.; Ivanova, A.; Polishchuk, P.,
EasyDock: customizable and scalable docking tool.
Journal of Cheminformatics 2023, 15 (1), 102.
https://doi.org/10.1186/s13321-023-00772-2