Common Molecular Docking Pitfalls: Mistakes That Invalidate Results

By BioDockify Computational Research Team · August 10, 2026 · Critical Analysis

Six common mistakes in molecular docking that produce misleading results. Covers protonation, water molecules, rigid receptor assumptions, solvation, and score interpretation.

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).
• Warren, G.L. et al. A critical assessment of docking programs and scoring functions. J. Med. Chem. 49, 5912-5931 (2006).

Scope & Limitations

These pitfalls apply to all docking engines Avoiding them improves but does not guarantee accurate results Experimental validation is always required