Speaker
Description
EasyDock 1.0 - an open-source and scalable Python-based tool for fully automated molecular docking. The current version supports popular docking programs, namely Autodock Vina, gnina, and smina. The tool automatically prepares ligands by removing salts, generating initial conformers and stereoisomers, using RDKit, and performing protonation with the open-source program MolGpKa. Ring sampling is implemented to improve docking of molecules containing saturated ring systems. All input data, settings, and results are stored in an SQLite database, enabling interrupted jobs to be resumed. EasyDock integrates Dask for distributed computation across multiple machines. A built-in model predicts docking times to optimize task scheduling and reduce total runtime. Special cases, such as boron-containing molecules, are handled by temporarily substituting boron with carbon during the docking process. The ProLIF package is integrated to calculate protein-ligand interactions. The current version is composed entirely of open-source modules.
