Dock

Dock is a cloud-based molecular docking platform that automates the preparation and execution of AutoDock Vina computations. Users enter a protein structure (via PDB ID or upload) and ligand structures (as SMILES strings or SDF files), and the platform automatically prepares the receptor and ligands, runs rigid-receptor docking, and generates results including affinity tables, 2D and 3D interaction diagrams, pose quality assessments, ADMET analysis, and publication-ready PDF reports.

The platform uses AutoDock Vina 1.2.7 with Meeko 0.7.1 for preparation, fixed docking settings (exhaustiveness 8, 9 modes), and includes PoseBusters pose validation and PLIP interaction profiling. It supports batch screening of up to 300 ligands per job with parallel Vina workers, optional co-crystal redock validation, customizable binding-site definition, and optional PyMOL visualization. All computations are performed securely in the cloud with data cleared after job completion.

The service includes interactive 3D visualization, sortable results tables with ADMET and interaction data, Methods text templates for manuscripts with numbered citations, and optional AI-assisted Discussion drafting. The platform is designed for students and researchers conducting molecular docking studies for coursework and publications.