EasyDock

EasyDock automates and scales molecular docking of small molecules across distributed computational nodes to enable screening of large compound libraries in drug discovery.

Key Features:

• Distributed Computing: Deploys over a network of computational nodes using the Dask library without requiring a specific cluster scheduler.
• Runtime Prediction: Implements a model that predicts docking experiment runtime to minimize overall docking time.
• Docking Engine Support: Supports Autodock Vina, gnina, smina, QVina2, Vina-GPU, CarsiDock, and SurfDock via a built-in client-server architecture.
• Boron-Containing Compounds: Enables docking of boron-containing compounds not inherently supported by Vina and smina.
• Ligand Preparation: Includes salt stripping, stereoisomer enumeration, and conformational sampling of saturated ring systems.
• Protonation Tools: Integrates open-source protonation tools pkasolver, MolGpKa, and Uni-pKa.
• Postdocking Analysis: Computes protein-ligand interaction fingerprints (PLIF) and assesses pose quality via PoseBusters.

Scientific Applications:

• Virtual Screening: Screens large compound collections to discover new chemical entities.
• De Novo Drug Design: Supports de novo design projects guided by molecular docking of large compound sets.
• Boron-Containing Ligand Docking: Validates docking of boron-containing compounds against PDB protein-ligand complexes.

Methodology:

EasyDock uses the Dask library for distributed deployment across computational nodes, implements a runtime prediction model to optimize scheduling, and processes ligands through preparation steps including salt stripping, stereoisomer enumeration, conformational sampling of saturated rings, and protonation before docking with supported engines.