EasyDock automates the entire docking process from molecule preparation to result analysis, supporting multiple docking programs and providing organized result storage.
- 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
# 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 --sdfhttps://easydock.readthedocs.io/en/latest/
BSD-3
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
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