Chemoinformatics tools
Institute of Molecular and Translational Medicine, Palacky University
EasyDock - fully automatic distributed docking pipeline
The open-source software to dock large chemical libraries in a distributed environment.
Features:
- the major script run_dock supports docking with vina and gnina (gnina also supports smina and its custom scoring functions)
- can be used as a command line utility or imported as a python module
- input molecules are checked for salts and attempted to fix by SaltRemover
- stereoisomers can be enumerated for unspecified chiral centers and double bonds
- several protonation options: chemaxon and pkasolver (check notes below)
- supports distributed computing using dask library
- supports docking of boron-containing compounds using vina and smina (boron is replaced with carbon before docking and returned back)
- all outputs are stored in an SQLite database
- interrupted calculations can be continued by invoking the same command or by supplying just a single argument - the existing output database
- get_sdf_from_dock_db is used to extract data from output DB
Repository:
https://github.com/ci-lab-cz/easydockCitation:
Minibaeva, G.; Ivanova, A.; Polishchuk, P. EasyDock: customizable and scalable docking tool. J. Cheminf. 2023, 15 (1), 102. - https://doi.org/10.1186/s13321-023-00772-2