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
• Server-Based Docking: Containerized docking programs (CarsiDock, SurfDock, Vina-GPU) via a persistent server protocol
• Generic Docking: Run external docking binary or Python script via a YAML config file, without code changes
• Automated Preparation: Molecule validation, salt removal, and stereoisomer enumeration
• Flexible Protonation: Multiple methods including MolGpKa, Uni-pKa, Chemaxon, and pkasolver
• Container Support: Run docking and protonation tools through Apptainer/Singularity or Docker with automatic GPU detection
• Distributed Computing: Scale across multiple servers using Dask
• Database Storage: All results organized in SQLite databases
• Pose Quality Assessment: PoseBusters integration (easydock_bust) for physics-based validation of docked poses
• PLIF Analysis: Protein-ligand interaction fingerprints (easydock_plif) 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

Third-party tools

EasyDock integrates several external tools, each governed by its own license. See the full license list in the documentation.

• Most docking programs and protonation tools are Apache 2.0 or MIT
• Chemaxon requires a commercial license
• Meeko is LGPL-2.1

Citation

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

2. EasyDock 1.3: An Automated Pipeline for Molecular Docking.
   Minibaeva, G.; Yap, V.; Polishchuk, P.
   J. Chem. Inf. Model. 2026.
   https://doi.org/10.1021/acs.jcim.6c01221