What Is Molecular Docking and How Does It Predict Protein-Ligand Binding?

By BioDockify Computational Research Team · August 8, 2026 · Molecular Docking

A beginner-friendly explanation of molecular docking \u2014 how computers predict how drugs bind to proteins. Covers lock-and-key model, scoring functions, a 6-step workflow, and real-world applications in drug discovery.

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

Key References

• Trott, O. & Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking. J. Comput. Chem. 31, 455-461 (2010). DOI: 10.1002/jcc.21334
• McNutt, A.T. et al. GNINA: molecular docking with deep learning. J. Cheminform. 13, 43 (2021). DOI: 10.1186/s13321-021-00522-2
• Kitchen, D.B. Docking and scoring in virtual screening for drug discovery. Drug Discov. Today 9, 993-1000 (2004).
• Li, H. et al. RF-Score v3: improved model for predicting protein-ligand affinity. J. Cheminform. 12, 20 (2020). DOI: 10.1186/s13321-020-00425-4
• Lengauer, T. & Rarey, M. Computational methods for biomolecular docking. Curr. Opin. Struct. Biol. 6, 402-406 (1996).
• Morris, G.M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785-2791 (2009). DOI: 10.1002/jcc.21256
• Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000). DOI: 10.1093/nar/28.1.235

Scope & Limitations

Docking scores are approximations, not experimental binding affinities Protein flexibility is limited in standard docking Solvent effects are simplified