Protein-Ligand Docking: A Complete Workflow for Pharmaceutical Research

By BioDockify Computational Research Team · August 8, 2026 · Workflow

A step-by-step research workflow for protein-ligand docking in drug discovery. Covers target selection, protein preparation, ligand preparation, docking execution, analysis, and validation with BioDockify.

Read the complete article with tables, code and references on BioDockify.

Key References

• Trott, O. & Olson, A.J. AutoDock Vina. J. Comput. Chem. 31, 455-461 (2010).
• McNutt, A.T. et al. GNINA. J. Cheminform. 13, 43 (2021).
• Irwin, J.J. et al. ZINC20. J. Chem. Inf. Model. 60, 2781-2790 (2020).

Scope & Limitations

Workflow assumes well-resolved crystal structure is available Homology models introduce additional uncertainty Automatic binding site detection may miss allosteric sites